issues: 279832457

Problem description

Under certain conditions, the netCDF files produced by Dataset.to_netcdf() have the wrong coordinates attributed to the variables. This seems to happen if there are multiple multi-dimensional coordinates, which share some (but not all) dimensions.

Test Dataset

Some sample code to generate a problematic Dataset:

```python import xarray as xr import numpy as np

zeros1 = np.zeros((5,3)) zeros2 = np.zeros((6,3)) zeros3 = np.zeros((5,4)) d = xr.Dataset({ 'lon1': (['x1','y1'], zeros1, {}), 'lon2': (['x2','y1'], zeros2, {}), 'lon3': (['x1','y2'], zeros3, {}), 'lat1': (['x1','y1'], zeros1, {}), 'lat2': (['x2','y1'], zeros2, {}), 'lat3': (['x1','y2'], zeros3, {}), 'foo1': (['x1','y1'], zeros1, {'coordinates': 'lon1 lat1'}), 'foo2': (['x2','y1'], zeros2, {'coordinates': 'lon2 lat2'}), 'foo3': (['x1','y2'], zeros3, {'coordinates': 'lon3 lat3'}), }) d = xr.conventions.decode_cf(d) Here, the coordinates lat1,lat2,lat3 (and lon1,lon2,lon3) share one dimension with each other. The Dataset itself gets created properly:

print(d)

<xarray.Dataset> Dimensions: (x1: 5, x2: 6, y1: 3, y2: 4) Coordinates: lat1 (x1, y1) float64 ... lat3 (x1, y2) float64 ... lat2 (x2, y1) float64 ... lon1 (x1, y1) float64 ... lon3 (x1, y2) float64 ... lon2 (x2, y1) float64 ... Dimensions without coordinates: x1, x2, y1, y2 Data variables: foo1 (x1, y1) float64 ... foo2 (x2, y1) float64 ... foo3 (x1, y2) float64 ... and each DataArray does have the right coordinates associated with them:

print (d.foo1)

<xarray.DataArray 'foo1' (x1: 5, y1: 3)> array([[ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.]]) Coordinates: lat1 (x1, y1) float64 ... lon1 (x1, y1) float64 ... Dimensions without coordinates: x1, y1

print (d.foo2)

<xarray.DataArray 'foo2' (x2: 6, y1: 3)> array([[ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.]]) Coordinates: lat2 (x2, y1) float64 ... lon2 (x2, y1) float64 ... Dimensions without coordinates: x2, y1

print (d.foo3)

<xarray.DataArray 'foo3' (x1: 5, y2: 4)> array([[ 0., 0., 0., 0.], [ 0., 0., 0., 0.], [ 0., 0., 0., 0.], [ 0., 0., 0., 0.], [ 0., 0., 0., 0.]]) Coordinates: lat3 (x1, y2) float64 ... lon3 (x1, y2) float64 ... Dimensions without coordinates: x1, y2

```

The problem

The problem happens when I try to write this to netCDF (using either the netCDF4 or scipy engines): python d.to_netcdf("test.nc") The resulting file has extra coordinates on the variables: ``` ~$ ncdump -h test.nc netcdf test { dimensions: x1 = 5 ; y1 = 3 ; y2 = 4 ; x2 = 6 ; variables: double lat1(x1, y1) ; lat1:_FillValue = NaN ; double lat3(x1, y2) ; lat3:_FillValue = NaN ; double lat2(x2, y1) ; lat2:_FillValue = NaN ; double lon1(x1, y1) ; lon1:_FillValue = NaN ; double lon3(x1, y2) ; lon3:_FillValue = NaN ; double lon2(x2, y1) ; lon2:_FillValue = NaN ; double foo1(x1, y1) ; foo1:_FillValue = NaN ; foo1:coordinates = "lat1 lat3 lat2 lon1 lon3 lon2" ; double foo2(x2, y1) ; foo2:_FillValue = NaN ; foo2:coordinates = "lon1 lon2 lat1 lat2" ; double foo3(x1, y2) ; foo3:_FillValue = NaN ; foo3:coordinates = "lon1 lon3 lat1 lat3" ;

// global attributes: :_NCProperties = "version=1|netcdflibversion=4.4.1.1|hdf5libversion=1.8.18" ; } ```

Here, foo1, foo2, and foo3 have extra coordinates associated with them. Interestingly, if I re-open this netCDF file with xarray.open_dataset, I get the correct coordinates back for each DataArray. However, other netCDF utilities may not be so forgiving.

Expected Output

I would expect the netCDF file to have a single pair of lat/lon for each variable: ... double foo1(x1, y1) ; foo1:_FillValue = NaN ; foo1:coordinates = "lat1 lon1" ; double foo2(x2, y1) ; foo2:_FillValue = NaN ; foo2:coordinates = "lon2 lat2" ; double foo3(x1, y2) ; foo3:_FillValue = NaN ; foo3:coordinates = "lon3 lat3" ; ... }

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: c2b205f29467a4431baa80b5c07fe31bda67fbef python: 2.7.12.final.0 python-bits: 64 OS: Linux OS-release: 4.4.0-101-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: None.None xarray: 0.10.0-5-gc2b205f pandas: 0.21.0 numpy: 1.13.3 scipy: None netCDF4: 1.3.1 h5netcdf: None Nio: None bottleneck: None cyordereddict: None dask: None matplotlib: None cartopy: None seaborn: None setuptools: 38.2.4 pip: 9.0.1 conda: None pytest: 3.3.1 IPython: None sphinx: None