psyplot · Chilipp · Apr 8, 2020 · Apr 8, 2020 · Apr 8, 2020 · Apr 8, 2020
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -9,7 +9,7 @@ see `#17 <https://github.com/psyplot/psyplot/pull/17>`__
     with psy.plot.mapplot('file.nc') as sp:
       sp.export('output.png')
 
-  sp will be closed automatically (see commit `ee7415b <https://github.com/psyplot/psyplot/commit/ee7415befce61247b5a08d9cfafab96ceb06f6f8>`__)
+  sp will be closed automatically (see `#18 <https://github.com/psyplot/psyplot/pull/18>`__)
 
 Changed
 -------
@@ -18,6 +18,8 @@ Changed
 * Specifying names in `x`, `y`, `t` and `z` attributes of the `CFDecoder` class
   now means that any other attribute (such as the `coordinates` or `axis` attribute)
   are ignored
+* If a given variable cannot be found in the provided coords to ``CFDecoder.get_variable_by_axis``,
+  we fall back to the ``CFDecoder.ds.coords`` attribute, see `#19 <https://github.com/psyplot/psyplot/pull/19>`__
 
 
 v1.2.1

diff --git a/psyplot/data.py b/psyplot/data.py
@@ -905,6 +905,23 @@ def get_variable_by_axis(self, var, axis, coords=None):
         See Also
         --------
         get_x, get_y, get_z, get_t"""
+
+        def get_coord(cname, raise_error=True):
+            try:
+                return coords[cname]
+            except KeyError:
+                if cname not in self.ds.coords:
+                    if raise_error:
+                        raise
+                    return None
+                ret = self.ds.coords[cname]
+                try:
+                    idims = var.psy.idims
+                except AttributeError:  # got xarray.Variable
+                    idims = {}
+                return ret.isel(**{d: sl for d, sl in idims.items()
+                                   if d in ret.dims})
+
         axis = axis.lower()
         if axis not in list('xyzt'):
             raise ValueError("Axis must be one of X, Y, Z, T, not {0}".format(
@@ -949,23 +966,23 @@ def get_variable_by_axis(self, var, axis, coords=None):
         if axis == 'x':
             for cname in filter(lambda cname: re.search('lon', cname),
                                 coord_names):
-                return coords[cname]
-            return coords.get(coord_names[-1])
+                return get_coord(cname)
+            return get_coord(coord_names[-1], raise_error=False)
         elif axis == 'y' and len(coord_names) >= 2:
             for cname in filter(lambda cname: re.search('lat', cname),
                                 coord_names):
-                return coords[cname]
-            return coords.get(coord_names[-2])
+                return get_coord(cname)
+            return get_coord(coord_names[-2], raise_error=False)
         elif (axis == 'z' and len(coord_names) >= 3 and
               coord_names[-3] not in tnames):
-            return coords.get(coord_names[-3])
+            return get_coord(coord_names[-3], raise_error=False)
         elif axis == 't' and tnames:
             tname = next(iter(tnames))
             if len(tnames) > 1:
                 warn("Found multiple matches for time coordinate in the "
                      "coordinates: %s. I use %s" % (', '.join(tnames), tname),
                      PsyPlotRuntimeWarning)
-            return coords.get(tname)
+            return get_coord(tname, raise_error=False)
 
     @docstrings.get_sectionsf("CFDecoder.get_x", sections=[
         'Parameters', 'Returns'])

diff --git a/tests/test_data.py b/tests/test_data.py
@@ -346,6 +346,19 @@ def test_get_variable_by_axis(self):
         # close the dataset
         ds.close()
 
+    def test_get_variable_by_axis_02(self):
+        """Test the :meth:`CFDecoder.get_variable_by_axis` method with missing
+        coordinates, see https://github.com/psyplot/psyplot/pull/19"""
+        fname = os.path.join(bt.test_dir, 'icon_test.nc')
+        with psyd.open_dataset(fname) as ds:
+            ds['ncells'] = ('ncells', np.arange(ds.dims['ncells']))
+            decoder = psyd.CFDecoder(ds)
+            arr = ds.psy['t2m'].psy.isel(ncells=slice(3, 10))
+            del arr['clon']
+            xcoord = decoder.get_variable_by_axis(arr, 'x', arr.coords)
+            self.assertEqual(xcoord.name, 'clon')
+            self.assertEqual(list(xcoord.ncells), list(arr.ncells))
+
     def test_plot_bounds_1d(self):
         """Test to get 2d-interval breaks"""
         x = xr.Variable(('x', ), np.arange(1, 5))