PERF: performance improvements in multi-key groupby

doc/source/whatsnew/v0.16.0.txt

@@ -174,6 +174,7 @@ Performance
 - Performance improvement of up to 10x in ``DataFrame.count`` and ``DataFrame.dropna`` by taking advantage of homogeneous/heterogeneous dtypes appropriately (:issue:`9136`)
 - Performance improvement of up to 20x in ``DataFrame.count`` when using a ``MultiIndex`` and the ``level`` keyword argument  (:issue:`9163`)
 - Performance and memory usage improvements in ``merge`` when key space exceeds ``int64`` bounds (:issue:`9151`)
+- Performance improvements in multi-key ``groupby`` (:issue:`9429`)
 
 Bug Fixes
 ~~~~~~~~~

pandas/core/groupby.py

@@ -1217,11 +1217,9 @@ class BaseGrouper(object):
     """
 
     def __init__(self, axis, groupings, sort=True, group_keys=True):
-        self.axis = axis
-        self.groupings = groupings
-        self.sort = sort
-        self.group_keys = group_keys
-        self.compressed = True
+        self._filter_empty_groups = self.compressed = len(groupings) != 1
+        self.axis, self.groupings, self.sort, self.group_keys = \
+                axis, groupings, sort, group_keys
 
     @property
     def shape(self):
@@ -1373,31 +1371,34 @@ def _get_compressed_labels(self):
             return _compress_group_index(group_index)
 
         ping = self.groupings[0]
-        self.compressed = False
-        self._filter_empty_groups = False
-
         return ping.labels, np.arange(len(ping.group_index))
 
     @cache_readonly
     def ngroups(self):
         return len(self.result_index)
 
+    @property
+    def recons_labels(self):
+        comp_ids, obs_ids, _ = self.group_info
+        labels = (ping.labels for ping in self.groupings)
+        return decons_obs_group_ids(comp_ids, obs_ids, self.shape, labels)
+
     @cache_readonly
     def result_index(self):
-        recons = self.get_group_levels()
-        return MultiIndex.from_arrays(recons, names=self.names)
+        if not self.compressed and len(self.groupings) == 1:
+            return self.groupings[0].group_index.rename(self.names[0])
 
-    def get_group_levels(self):
-        comp_ids, obs_ids, _ = self.group_info
+        return MultiIndex(levels=[ping.group_index for ping in self.groupings],
+                          labels=self.recons_labels,
+                          verify_integrity=False,
+                          names=self.names)
 
+    def get_group_levels(self):
         if not self.compressed and len(self.groupings) == 1:
             return [self.groupings[0].group_index]
 
-        recons_labels = decons_obs_group_ids(comp_ids, obs_ids,
-                self.shape, (ping.labels for ping in self.groupings))
-
         name_list = []
-        for ping, labels in zip(self.groupings, recons_labels):
+        for ping, labels in zip(self.groupings, self.recons_labels):
             labels = com._ensure_platform_int(labels)
             levels = ping.group_index.take(labels)
 
@@ -1432,8 +1433,6 @@ def get_group_levels(self):
 
     _name_functions = {}
 
-    _filter_empty_groups = True
-
     def _get_aggregate_function(self, how, values):
 
         dtype_str = values.dtype.name
@@ -1797,8 +1796,6 @@ def size(self):
         'ohlc': lambda *args: ['open', 'high', 'low', 'close']
     }
 
-    _filter_empty_groups = True
-
     def _aggregate(self, result, counts, values, how, is_numeric=True):
 
         agg_func, dtype = self._get_aggregate_function(how, values)

vb_suite/groupby.py

@@ -501,6 +501,25 @@ def f(g):
 groupby_int64_overflow = Benchmark("df.groupby(list('abcde')).max()", setup,
                                    name='groupby_int64_overflow')
 
+
+setup = common_setup + '''
+from itertools import product
+from string import ascii_letters, digits
+
+n = 5 * 7 * 11 * (1 << 9)
+alpha = list(map(''.join, product(ascii_letters + digits, repeat=4)))
+f = lambda k: np.repeat(np.random.choice(alpha, n // k), k)
+
+df = DataFrame({'a': f(11), 'b': f(7), 'c': f(5), 'd': f(1)})
+df['joe'] = (np.random.randn(len(df)) * 10).round(3)
+
+i = np.random.permutation(len(df))
+df = df.iloc[i].reset_index(drop=True).copy()
+'''
+
+groupby_multi_index = Benchmark("df.groupby(list('abcd')).max()", setup,
+                                name='groupby_multi_index')
+
 #----------------------------------------------------------------------
 # groupby with a variable value for ngroups