Clessig/develop/fix empty io 819 2 (ecmwf#822)

* Fix to io problems.

* Fix issues in input

Author: clessig

packages/common/src/weathergen/common/io.py

@@ -153,8 +153,8 @@ def as_xarray(self, chunk_nsamples=CHUNK_N_SAMPLES) -> xr.Dataset:
                 "ipoint": self.datapoints,
                 "channel": self.channels,  # TODO: make sure channel names align with data
                 "valid_time": ("ipoint", times.astype("datetime64[ns]")),
-                "lat": ("ipoint", coords[:, 0]),
-                "lon": ("ipoint", coords[:, 1]),
+                "lat": ("ipoint", coords[..., 0]),
+                "lon": ("ipoint", coords[..., 1]),
                 **geoinfo,
             },
             name=self.name,
@@ -436,6 +436,9 @@ def _offset_key(self, key: ItemKey):
 
     def _extract_coordinates(self, stream_idx, offset_key, datapoints) -> DataCoordinates:
         _coords = self.targets_coords[offset_key.forecast_step][stream_idx][datapoints].numpy()
+        # ensure _coords has size (?,2)
+        if len(_coords) == 0:
+            _coords = np.zeros((0, 2), dtype=np.float32)
         coords = _coords[..., :2]  # first two columns are lat,lon
         geoinfo = _coords[..., 2:]  # the rest is geoinfo => potentially empty
         if geoinfo.size > 0:  # TODO: set geoinfo to be empty for now