PERF/BUG: reimplement MultiIndex.remove_unused_levels

asv_bench/benchmarks/indexing.py

@@ -204,6 +204,12 @@ def setup(self):
             [np.arange(100), list('A'), list('A')],
             names=['one', 'two', 'three'])
 
+        rng = np.random.RandomState(4)
+        size = 1 << 16
+        self.mi_unused_levels = pd.MultiIndex.from_arrays([
+            rng.randint(0, 1 << 13, size),
+            rng.randint(0, 1 << 10, size)])[rng.rand(size) < 0.1]
+
     def time_series_xs_mi_ix(self):
         self.s.ix[999]
 
@@ -248,6 +254,9 @@ def time_multiindex_small_get_loc_warm(self):
     def time_is_monotonic(self):
         self.miint.is_monotonic
 
+    def time_remove_unused_levels(self):
+        self.mi_unused_levels.remove_unused_levels()
+
 
 class IntervalIndexing(object):
     goal_time = 0.2

doc/source/whatsnew/v0.20.2.txt

@@ -32,6 +32,7 @@ Performance Improvements
 - Performance regression fix for MultiIndexes (:issue:`16319`, :issue:`16346`)
 - Improved performance of ``.clip()`` with scalar arguments (:issue:`15400`)
 - Improved performance of groupby with categorical groupers (:issue:`16413`)
+- Improved performance of ``MultiIndex.remove_unused_levels()`` (:issue:`16556`)
 
 .. _whatsnew_0202.bug_fixes:
 
@@ -61,6 +62,7 @@ Indexing
 
 - Bug in ``DataFrame.reset_index(level=)`` with single level index (:issue:`16263`)
 - Bug in partial string indexing with a monotonic, but not strictly-monotonic, index incorrectly reversing the slice bounds (:issue:`16515`)
+- Bug in ``MultiIndex.remove_unused_levels()`` (:issue:`16556`)
 
 I/O
 ^^^

pandas/core/indexes/multi.py

@@ -1290,42 +1290,38 @@ def remove_unused_levels(self):
         new_levels = []
         new_labels = []
 
-        changed = np.ones(self.nlevels, dtype=bool)
-        for i, (lev, lab) in enumerate(zip(self.levels, self.labels)):
+        changed = False
+        for lev, lab in zip(self.levels, self.labels):
 
             uniques = algos.unique(lab)
 
             # nothing unused
             if len(uniques) == len(lev):
                 new_levels.append(lev)
                 new_labels.append(lab)
-                changed[i] = False
                 continue
 
-            # set difference, then reverse sort
-            diff = Index(np.arange(len(lev))).difference(uniques)
-            unused = diff.sort_values(ascending=False)
+            changed = True
+
+            # labels get mapped from uniques to 0:len(uniques)
+            label_mapping = np.zeros(len(lev))
+            label_mapping[uniques] = np.arange(len(uniques))
+            lab = label_mapping[lab]
 
             # new levels are simple
             lev = lev.take(uniques)
 
-            # new labels, we remove the unsued
-            # by decrementing the labels for that value
-            # prob a better way
-            for u in unused:
-
-                lab = np.where(lab > u, lab - 1, lab)
-
             new_levels.append(lev)
             new_labels.append(lab)
 
-        # nothing changed
-        if not changed.any():
-            return self
+        result = self._shallow_copy()
 
-        return MultiIndex(new_levels, new_labels,
-                          names=self.names, sortorder=self.sortorder,
-                          verify_integrity=False)
+        if changed:
+            result._reset_identity()
+            result._set_levels(new_levels, validate=False)
+            result._set_labels(new_labels, validate=False)
+
+        return result
 
     @property
     def nlevels(self):

pandas/tests/indexes/test_multi.py

@@ -2515,7 +2515,34 @@ def test_reconstruct_remove_unused(self):
         # idempotent
         result2 = result.remove_unused_levels()
         tm.assert_index_equal(result2, expected)
-        assert result2 is result
+        assert result2.is_(result)
+
+    @pytest.mark.parametrize('first_type,second_type', [
+        ('int64', 'int64'),
+        ('datetime64[D]', 'str')])
+    def test_remove_unused_levels_large(self, first_type, second_type):
+        # GH16556
+
+        # because tests should be deterministic (and this test in particular
+        # checks that levels are removed, which is not the case for every
+        # random input):
+        rng = np.random.RandomState(4)  # seed is arbitrary value that works
+
+        size = 1 << 16
+        df = DataFrame(dict(
+            first=rng.randint(0, 1 << 13, size).astype(first_type),
+            second=rng.randint(0, 1 << 10, size).astype(second_type),
+            third=rng.rand(size)))
+        df = df.groupby(['first', 'second']).sum()
+        df = df[df.third < 0.1]
+
+        result = df.index.remove_unused_levels()
+        assert len(result.levels[0]) < len(df.index.levels[0])
+        assert len(result.levels[1]) < len(df.index.levels[1])
+        assert result.equals(df.index)
+
+        expected = df.reset_index().set_index(['first', 'second']).index
+        tm.assert_index_equal(result, expected)
 
     def test_isin(self):
         values = [('foo', 2), ('bar', 3), ('quux', 4)]