Fix multiple grouping with missing groups

doc/whats-new.rst

@@ -68,6 +68,8 @@ Bug fixes
 - Fix the safe_chunks validation option on the to_zarr method
   (:issue:`5511`, :pull:`9559`). By `Joseph Nowak
   <https://github.com/josephnowak>`_.
+- Fix binning by multiple variables where some bins have no observations. (:issue:`9630`).
+  By `Deepak Cherian <https://github.com/dcherian>`_.
 
 Documentation
 ~~~~~~~~~~~~~

xarray/core/dataarray.py

@@ -6808,7 +6808,7 @@ def groupby(
 
         >>> da.groupby("letters")
         <DataArrayGroupBy, grouped over 1 grouper(s), 2 groups in total:
-            'letters': 2 groups with labels 'a', 'b'>
+            'letters': 2/2 groups present with labels 'a', 'b'>
 
         Execute a reduction
 
@@ -6824,8 +6824,8 @@ def groupby(
 
         >>> da.groupby(["letters", "x"])
         <DataArrayGroupBy, grouped over 2 grouper(s), 8 groups in total:
-            'letters': 2 groups with labels 'a', 'b'
-            'x': 4 groups with labels 10, 20, 30, 40>
+            'letters': 2/2 groups present with labels 'a', 'b'
+            'x': 4/4 groups present with labels 10, 20, 30, 40>
 
         Use Grouper objects to express more complicated GroupBy operations
 

xarray/core/dataset.py

@@ -10403,7 +10403,7 @@ def groupby(
 
         >>> ds.groupby("letters")
         <DatasetGroupBy, grouped over 1 grouper(s), 2 groups in total:
-            'letters': 2 groups with labels 'a', 'b'>
+            'letters': 2/2 groups present with labels 'a', 'b'>
 
         Execute a reduction
 
@@ -10420,8 +10420,8 @@ def groupby(
 
         >>> ds.groupby(["letters", "x"])
         <DatasetGroupBy, grouped over 2 grouper(s), 8 groups in total:
-            'letters': 2 groups with labels 'a', 'b'
-            'x': 4 groups with labels 10, 20, 30, 40>
+            'letters': 2/2 groups present with labels 'a', 'b'
+            'x': 4/4 groups present with labels 10, 20, 30, 40>
 
         Use Grouper objects to express more complicated GroupBy operations
 

xarray/core/groupby.py

@@ -454,6 +454,7 @@ def factorize(self) -> EncodedGroups:
         # At this point all arrays have been factorized.
         codes = tuple(grouper.codes for grouper in groupers)
         shape = tuple(grouper.size for grouper in groupers)
+        masks = tuple((code == -1) for code in codes)
         # We broadcast the codes against each other
         broadcasted_codes = broadcast(*codes)
         # This fully broadcasted DataArray is used as a template later
@@ -464,24 +465,18 @@ def factorize(self) -> EncodedGroups:
         )
         # NaNs; as well as values outside the bins are coded by -1
         # Restore these after the raveling
-        mask = functools.reduce(
-            np.logical_or,  # type: ignore[arg-type]
-            [(code == -1) for code in broadcasted_codes],
-        )
+        broadcasted_masks = broadcast(*masks)
+        mask = functools.reduce(np.logical_or, broadcasted_masks)  # type: ignore[arg-type]
         _flatcodes[mask] = -1
 
-        midx = pd.MultiIndex.from_product(
-            (grouper.unique_coord.data for grouper in groupers),
+        full_index = pd.MultiIndex.from_product(
+            (grouper.full_index.values for grouper in groupers),
             names=tuple(grouper.name for grouper in groupers),
         )
         # Constructing an index from the product is wrong when there are missing groups
         # (e.g. binning, resampling). Account for that now.
-        midx = midx[np.sort(pd.unique(_flatcodes[~mask]))]
+        midx = full_index[np.sort(pd.unique(_flatcodes[~mask]))]
 
-        full_index = pd.MultiIndex.from_product(
-            (grouper.full_index.values for grouper in groupers),
-            names=tuple(grouper.name for grouper in groupers),
-        )
         dim_name = "stacked_" + "_".join(str(grouper.name) for grouper in groupers)
 
         coords = Coordinates.from_pandas_multiindex(midx, dim=dim_name)
@@ -684,7 +679,7 @@ def __repr__(self) -> str:
         for grouper in self.groupers:
             coord = grouper.unique_coord
             labels = ", ".join(format_array_flat(coord, 30).split())
-            text += f"\n    {grouper.name!r}: {coord.size} groups with labels {labels}"
+            text += f"\n    {grouper.name!r}: {coord.size}/{grouper.full_index.size} groups present with labels {labels}"
         return text + ">"
 
     def _iter_grouped(self) -> Iterator[T_Xarray]:

xarray/tests/test_groupby.py

@@ -585,7 +585,7 @@ def test_groupby_repr(obj, dim) -> None:
     N = len(np.unique(obj[dim]))
     expected = f"<{obj.__class__.__name__}GroupBy"
     expected += f", grouped over 1 grouper(s), {N} groups in total:"
-    expected += f"\n    {dim!r}: {N} groups with labels "
+    expected += f"\n    {dim!r}: {N}/{N} groups present with labels "
     if dim == "x":
         expected += "1, 2, 3, 4, 5>"
     elif dim == "y":
@@ -602,7 +602,7 @@ def test_groupby_repr_datetime(obj) -> None:
     actual = repr(obj.groupby("t.month"))
     expected = f"<{obj.__class__.__name__}GroupBy"
     expected += ", grouped over 1 grouper(s), 12 groups in total:\n"
-    expected += "    'month': 12 groups with labels "
+    expected += "    'month': 12/12 groups present with labels "
     expected += "1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12>"
     assert actual == expected
 
@@ -2932,3 +2932,35 @@ def test_groupby_transpose():
     second = data.groupby("x").sum()
 
     assert_identical(first, second.transpose(*first.dims))
+
+
+def test_groupby_multiple_bin_grouper_missing_groups():
+    from numpy import nan
+
+    ds = xr.Dataset(
+        {"foo": (("z"), np.arange(12))},
+        coords={"x": ("z", np.arange(12)), "y": ("z", np.arange(12))},
+    )
+
+    actual = ds.groupby(
+        x=BinGrouper(np.arange(0, 13, 4)), y=BinGrouper(bins=np.arange(0, 16, 2))
+    ).count()
+    expected = Dataset(
+        {
+            "foo": (
+                ("x_bins", "y_bins"),
+                np.array(
+                    [
+                        [2.0, 2.0, nan, nan, nan, nan, nan],
+                        [nan, nan, 2.0, 2.0, nan, nan, nan],
+                        [nan, nan, nan, nan, 2.0, 1.0, nan],
+                    ]
+                ),
+            )
+        },
+        coords={
+            "x_bins": ("x_bins", pd.IntervalIndex.from_breaks(np.arange(0, 13, 4))),
+            "y_bins": ("y_bins", pd.IntervalIndex.from_breaks(np.arange(0, 16, 2))),
+        },
+    )
+    assert_identical(actual, expected)