Fixes #3762: Fix dataframe groupby aggregations when keys contain NaNs

arkouda/dataframe.py

@@ -4,6 +4,7 @@
 import os
 import random
 from collections import UserDict
+from functools import reduce
 from typing import Callable, Dict, List, Optional, Tuple, Union, cast
 from warnings import warn
 
@@ -24,10 +25,11 @@
 from arkouda.join import inner_join
 from arkouda.numpy import cast as akcast
 from arkouda.numpy import cumsum, where
-from arkouda.numpy.dtypes import bigint
+from arkouda.numpy.dtypes import _is_dtype_in_union, bigint
 from arkouda.numpy.dtypes import bool_ as akbool
 from arkouda.numpy.dtypes import float64 as akfloat64
 from arkouda.numpy.dtypes import int64 as akint64
+from arkouda.numpy.dtypes import numeric_scalars
 from arkouda.numpy.dtypes import uint64 as akuint64
 from arkouda.pdarrayclass import RegistrationError, pdarray
 from arkouda.pdarraycreation import arange, array, create_pdarray, full, zeros
@@ -105,13 +107,47 @@ class DataFrameGroupBy:
  """
 
  def __init__(self, gb, df, gb_key_names=None, as_index=True):
+
  self.gb = gb
  self.df = df
  self.gb_key_names = gb_key_names
  self.as_index = as_index
  for attr in ["nkeys", "permutation", "unique_keys", "segments"]:
  setattr(self, attr, getattr(gb, attr))
 
+ self.dropna = self.gb.dropna
+ self.where_not_nan = None
+ self.all_non_nan = False
+
+ if self.dropna:
+ from arkouda import all as ak_all
+ from arkouda import isnan
+
+ # calculate ~isnan on each key then & them all together
+ # keep up with if they're all_non_nan, so we can skip indexing later
+ key_cols = (
+ [df[k] for k in gb_key_names] if isinstance(gb_key_names, List) else [df[gb_key_names]]
+ )
+ where_key_not_nan = [
+ ~isnan(col)
+ for col in key_cols
+ if isinstance(col, pdarray) and _is_dtype_in_union(col.dtype, numeric_scalars)
+ ]
+
+ if len(where_key_not_nan) == 0:
+ # if empty then none of the keys are pdarray, so non are nan
+ self.all_non_nan = True
+ else:
+ self.where_not_nan = reduce(lambda x, y: x & y, where_key_not_nan)
+ self.all_non_nan = ak_all(self.where_not_nan)
+
+ def _get_df_col(self, c):
+ # helper function to mask out the values where the keys are nan when dropna is True
+ if not self.dropna or self.all_non_nan:
+ return self.df.data[c]
+ else:
+ return self.df.data[c][self.where_not_nan]
+
  @classmethod
  def _make_aggop(cls, opname):
  numerical_dtypes = [akfloat64, akint64, akuint64]
@@ -148,18 +184,18 @@ def aggop(self, colnames=None):
  if isinstance(colnames, List):
  if isinstance(self.gb_key_names, str):
  return DataFrame(
- {c: self.gb.aggregate(self.df.data[c], opname)[1] for c in colnames},
+ {c: self.gb.aggregate(self._get_df_col(c), opname)[1] for c in colnames},
  index=Index(self.gb.unique_keys, name=self.gb_key_names),
  )
  elif isinstance(self.gb_key_names, list) and len(self.gb_key_names) == 1:
  return DataFrame(
- {c: self.gb.aggregate(self.df.data[c], opname)[1] for c in colnames},
+ {c: self.gb.aggregate(self._get_df_col(c), opname)[1] for c in colnames},
  index=Index(self.gb.unique_keys, name=self.gb_key_names[0]),
  )
  elif isinstance(self.gb_key_names, list):
  column_dict = dict(zip(self.gb_key_names, self.unique_keys))
  for c in colnames:
- column_dict[c] = self.gb.aggregate(self.df.data[c], opname)[1]
+ column_dict[c] = self.gb.aggregate(self._get_df_col(c), opname)[1]
  return DataFrame(column_dict)
  else:
  return None

tests/dataframe_test.py

@@ -1,7 +1,5 @@
-import glob
 import itertools
 import os
-import tempfile
 
 import numpy as np
 import pandas as pd
@@ -652,16 +650,47 @@ def test_gb_aggregations_example_numeric_types(self, agg):
  pd_result = getattr(pd_df.groupby(group_on), agg)()
  assert_frame_equal(ak_result.to_pandas(retain_index=True), pd_result)
 
+ @pytest.mark.parametrize("dropna", [True, False])
  @pytest.mark.parametrize("agg", ["count", "max", "mean", "median", "min", "std", "sum", "var"])
- def test_gb_aggregations_with_nans(self, agg):
+ def test_gb_aggregations_with_nans(self, agg, dropna):
  df = self.build_ak_df_with_nans()
  # @TODO handle bool columns correctly
  df.drop("bools", axis=1, inplace=True)
  pd_df = df.to_pandas()
 
  group_on = ["key1", "key2"]
- ak_result = getattr(df.groupby(group_on), agg)()
- pd_result = getattr(pd_df.groupby(group_on, as_index=False), agg)()
+ ak_result = getattr(df.groupby(group_on, dropna=dropna), agg)()
+ pd_result = getattr(pd_df.groupby(group_on, as_index=False, dropna=dropna), agg)()
+ assert_frame_equal(ak_result.to_pandas(retain_index=True), pd_result)
+
+ # TODO aggregations of string columns not currently supported (even for count)
+ df.drop("key1", axis=1, inplace=True)
+ df.drop("key2", axis=1, inplace=True)
+ pd_df = df.to_pandas()
+
+ group_on = ["nums1", "nums2"]
+ ak_result = getattr(df.groupby(group_on, dropna=dropna), agg)()
+ pd_result = getattr(pd_df.groupby(group_on, as_index=False, dropna=dropna), agg)()
+ assert_frame_equal(ak_result.to_pandas(retain_index=True), pd_result)
+
+ # TODO aggregation mishandling NaN see issue #3765
+ df.drop("nums2", axis=1, inplace=True)
+ pd_df = df.to_pandas()
+ group_on = "nums1"
+ ak_result = getattr(df.groupby(group_on, dropna=dropna), agg)()
+ pd_result = getattr(pd_df.groupby(group_on, dropna=dropna), agg)()
+ assert_frame_equal(ak_result.to_pandas(retain_index=True), pd_result)
+
+ @pytest.mark.parametrize("dropna", [True, False])
+ def test_count_nan_bug(self, dropna):
+ # verify reproducer for #3762 is fixed
+ df = ak.DataFrame({"A": [1, 2, 2, np.nan], "B": [3, 4, 5, 6], "C": [1, np.nan, 2, 3]})
+ ak_result = df.groupby("A", dropna=dropna).count()
+ pd_result = df.to_pandas().groupby("A", dropna=dropna).count()
+ assert_frame_equal(ak_result.to_pandas(retain_index=True), pd_result)
+
+ ak_result = df.groupby(["A", "C"], as_index=False, dropna=dropna).count()
+ pd_result = df.to_pandas().groupby(["A", "C"], as_index=False, dropna=dropna).count()
  assert_frame_equal(ak_result.to_pandas(retain_index=True), pd_result)
 
  def test_gb_aggregations_return_dataframe(self):