BUG: Fix segfault in GroupBy.count and DataFrame.count

doc/source/whatsnew/v1.1.0.rst

@@ -303,7 +303,7 @@ Numeric
 - Bug in :meth:`to_numeric` with string argument ``"uint64"`` and ``errors="coerce"`` silently fails (:issue:`32394`)
 - Bug in :meth:`to_numeric` with ``downcast="unsigned"`` fails for empty data (:issue:`32493`)
 - Bug in :meth:`DataFrame.mean` with ``numeric_only=False`` and either ``datetime64`` dtype or ``PeriodDtype`` column incorrectly raising ``TypeError`` (:issue:`32426`)
--
+- Bug in :meth:`DataFrame.count` with ``level="foo"`` and index level ``"foo"`` containing NaNs causes segmentation fault (:issue:`21824`)
 
 Conversion
 ^^^^^^^^^^
@@ -398,6 +398,7 @@ Groupby/resample/rolling
 
 - Bug in :meth:`GroupBy.apply` raises ``ValueError`` when the ``by`` axis is not sorted and has duplicates and the applied ``func`` does not mutate passed in objects (:issue:`30667`)
 - Bug in :meth:`DataFrameGroupby.transform` produces incorrect result with transformation functions (:issue:`30918`)
+- Bug in :meth:`GroupBy.count` causes segmentation fault when grouped-by column contains NaNs (:issue:`32841`)
 
 Reshaping
 ^^^^^^^^^

pandas/_libs/lib.pyx

@@ -793,14 +793,16 @@ def count_level_2d(ndarray[uint8_t, ndim=2, cast=True] mask,
         with nogil:
             for i in range(n):
                 for j in range(k):
-                    counts[labels[i], j] += mask[i, j]
+                    if mask[i, j]:
+                        counts[labels[i], j] += 1
 
     else:  # axis == 1
         counts = np.zeros((n, max_bin), dtype='i8')
         with nogil:
             for i in range(n):
                 for j in range(k):
-                    counts[i, labels[j]] += mask[i, j]
+                    if mask[i, j]:
+                        counts[i, labels[j]] += 1
 
     return counts
 

pandas/core/frame.py

@@ -7890,34 +7890,30 @@ def _count_level(self, level, axis=0, numeric_only=False):
                 f"Can only count levels on hierarchical {self._get_axis_name(axis)}."
             )
 
-        if frame._is_mixed_type:
-            # Since we have mixed types, calling notna(frame.values) might
-            # upcast everything to object
-            mask = notna(frame).values
-        else:
-            # But use the speedup when we have homogeneous dtypes
-            mask = notna(frame.values)
+        # Mask NaNs: Mask rows or columns where the index level is NaN, and all
+        # values in the DataFrame that are NaN
+        values_mask = notna(frame.values)
 
+        index_mask = notna(count_axis.get_level_values(level=level))
         if axis == 1:
-            # We're transposing the mask rather than frame to avoid potential
-            # upcasts to object, which induces a ~20x slowdown
-            mask = mask.T
+            mask = index_mask & values_mask
+        else:
+            mask = index_mask.reshape(-1, 1) & values_mask
 
         if isinstance(level, str):
             level = count_axis._get_level_number(level)
 
         level_name = count_axis._names[level]
         level_index = count_axis.levels[level]._shallow_copy(name=level_name)
         level_codes = ensure_int64(count_axis.codes[level])
-        counts = lib.count_level_2d(mask, level_codes, len(level_index), axis=0)
-
-        result = DataFrame(counts, index=level_index, columns=agg_axis)
+        counts = lib.count_level_2d(mask, level_codes, len(level_index), axis=axis)
 
         if axis == 1:
-            # Undo our earlier transpose
-            return result.T
+            result = DataFrame(counts, index=agg_axis, columns=level_index)
         else:
-            return result
+            result = DataFrame(counts, index=level_index, columns=agg_axis)
+
+        return result
 
     def _reduce(
         self, op, name, axis=0, skipna=True, numeric_only=None, filter_type=None, **kwds

pandas/tests/groupby/test_counting.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pytest
 
-from pandas import DataFrame, MultiIndex, Period, Series, Timedelta, Timestamp
+from pandas import DataFrame, Index, MultiIndex, Period, Series, Timedelta, Timestamp
 import pandas._testing as tm
 
 
@@ -220,3 +220,12 @@ def test_count_with_only_nans_in_first_group(self):
         mi = MultiIndex(levels=[[], ["a", "b"]], codes=[[], []], names=["A", "B"])
         expected = Series([], index=mi, dtype=np.int64, name="C")
         tm.assert_series_equal(result, expected, check_index_type=False)
+
+    def test_count_groupby_column_with_nan_in_groupby_column(self):
+        # https://github.com/pandas-dev/pandas/issues/32841
+        df = DataFrame({"A": [1, 1, 1, 1, 1], "B": [5, 4, np.NaN, 3, 0]})
+        res = df.groupby(["B"]).count()
+        expected = DataFrame(
+            index=Index([0.0, 3.0, 4.0, 5.0], name="B"), data={"A": [1, 1, 1, 1]}
+        )
+        tm.assert_frame_equal(expected, res)

pandas/tests/test_multilevel.py

@@ -248,6 +248,34 @@ def _check_counts(frame, axis=0):
         result = self.frame.count(level=0, numeric_only=True)
         tm.assert_index_equal(result.columns, Index(list("ABC"), name="exp"))
 
+    def test_count_index_with_nan(self):
+        # https://github.com/pandas-dev/pandas/issues/21824
+        df = DataFrame(
+            {
+                "Person": ["John", "Myla", None, "John", "Myla"],
+                "Age": [24.0, 5, 21.0, 33, 26],
+                "Single": [False, True, True, True, False],
+            }
+        )
+
+        # count on row labels
+        res = df.set_index(["Person", "Single"]).count(level="Person")
+        expected = DataFrame(
+            index=Index(["John", "Myla"], name="Person"),
+            columns=Index(["Age"]),
+            data=[2, 2],
+        )
+        tm.assert_frame_equal(res, expected)
+
+        # count on column labels
+        res = df.set_index(["Person", "Single"]).T.count(level="Person", axis=1)
+        expected = DataFrame(
+            columns=Index(["John", "Myla"], name="Person"),
+            index=Index(["Age"]),
+            data=[[2, 2]],
+        )
+        tm.assert_frame_equal(res, expected)
+
     def test_count_level_series(self):
         index = MultiIndex(
             levels=[["foo", "bar", "baz"], ["one", "two", "three", "four"]],