Duplicate Labels¶
Index objects are not required to be unique; you can have duplicate row
or column labels. This may be a bit confusing at first. If you’re familiar with
SQL, you know that row labels are similar to a primary key on a table, and you
would never want duplicates in a SQL table. But one of pandas’ roles is to clean
messy, real-world data before it goes to some downstream system. And real-world
data has duplicates, even in fields that are supposed to be unique.
This section describes how duplicate labels change the behavior of certain operations, and how prevent duplicates from arising during operations, or to detect them if they do.
In [1]: import pandas as pd
In [2]: import numpy as np
Consequences of Duplicate Labels¶
Some pandas methods (Series.reindex() for example) just don’t work with
duplicates present. The output can’t be determined, and so pandas raises.
In [3]: s1 = pd.Series([0, 1, 2], index=["a", "b", "b"])
In [4]: s1.reindex(["a", "b", "c"])
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [4], in <module>
----> 1 s1.reindex(["a", "b", "c"])
File /pandas/pandas/core/series.py:4672, in Series.reindex(self, *args, **kwargs)
4668 raise TypeError(
4669 "'index' passed as both positional and keyword argument"
4670 )
4671 kwargs.update({"index": index})
-> 4672 return super().reindex(**kwargs)
File /pandas/pandas/core/generic.py:4974, in NDFrame.reindex(self, *args, **kwargs)
4971 return self._reindex_multi(axes, copy, fill_value)
4973 # perform the reindex on the axes
-> 4974 return self._reindex_axes(
4975 axes, level, limit, tolerance, method, fill_value, copy
4976 ).__finalize__(self, method="reindex")
File /pandas/pandas/core/generic.py:4994, in NDFrame._reindex_axes(self, axes, level, limit, tolerance, method, fill_value, copy)
4989 new_index, indexer = ax.reindex(
4990 labels, level=level, limit=limit, tolerance=tolerance, method=method
4991 )
4993 axis = self._get_axis_number(a)
-> 4994 obj = obj._reindex_with_indexers(
4995 {axis: [new_index, indexer]},
4996 fill_value=fill_value,
4997 copy=copy,
4998 allow_dups=False,
4999 )
5000 # If we've made a copy once, no need to make another one
5001 copy = False
File /pandas/pandas/core/generic.py:5040, in NDFrame._reindex_with_indexers(self, reindexers, fill_value, copy, allow_dups)
5037 indexer = ensure_platform_int(indexer)
5039 # TODO: speed up on homogeneous DataFrame objects (see _reindex_multi)
-> 5040 new_data = new_data.reindex_indexer(
5041 index,
5042 indexer,
5043 axis=baxis,
5044 fill_value=fill_value,
5045 allow_dups=allow_dups,
5046 copy=copy,
5047 )
5048 # If we've made a copy once, no need to make another one
5049 copy = False
File /pandas/pandas/core/internals/managers.py:679, in BaseBlockManager.reindex_indexer(self, new_axis, indexer, axis, fill_value, allow_dups, copy, consolidate, only_slice, use_na_proxy)
677 # some axes don't allow reindexing with dups
678 if not allow_dups:
--> 679 self.axes[axis]._validate_can_reindex(indexer)
681 if axis >= self.ndim:
682 raise IndexError("Requested axis not found in manager")
File /pandas/pandas/core/indexes/base.py:4107, in Index._validate_can_reindex(self, indexer)
4105 # trying to reindex on an axis with duplicates
4106 if not self._index_as_unique and len(indexer):
-> 4107 raise ValueError("cannot reindex on an axis with duplicate labels")
ValueError: cannot reindex on an axis with duplicate labels
Other methods, like indexing, can give very surprising results. Typically
indexing with a scalar will reduce dimensionality. Slicing a DataFrame
with a scalar will return a Series. Slicing a Series with a scalar will
return a scalar. But with duplicates, this isn’t the case.
In [5]: df1 = pd.DataFrame([[0, 1, 2], [3, 4, 5]], columns=["A", "A", "B"])
In [6]: df1
Out[6]:
A A B
0 0 1 2
1 3 4 5
We have duplicates in the columns. If we slice 'B', we get back a Series
In [7]: df1["B"] # a series
Out[7]:
0 2
1 5
Name: B, dtype: int64
But slicing 'A' returns a DataFrame
In [8]: df1["A"] # a DataFrame
Out[8]:
A A
0 0 1
1 3 4
This applies to row labels as well
In [9]: df2 = pd.DataFrame({"A": [0, 1, 2]}, index=["a", "a", "b"])
In [10]: df2
Out[10]:
A
a 0
a 1
b 2
In [11]: df2.loc["b", "A"] # a scalar
Out[11]: 2
In [12]: df2.loc["a", "A"] # a Series
Out[12]:
a 0
a 1
Name: A, dtype: int64
Duplicate Label Detection¶
You can check whether an Index (storing the row or column labels) is
unique with Index.is_unique:
In [13]: df2
Out[13]:
A
a 0
a 1
b 2
In [14]: df2.index.is_unique
Out[14]: False
In [15]: df2.columns.is_unique
Out[15]: True
Note
Checking whether an index is unique is somewhat expensive for large datasets. pandas does cache this result, so re-checking on the same index is very fast.
Index.duplicated() will return a boolean ndarray indicating whether a
label is repeated.
In [16]: df2.index.duplicated()
Out[16]: array([False, True, False])
Which can be used as a boolean filter to drop duplicate rows.
In [17]: df2.loc[~df2.index.duplicated(), :]
Out[17]:
A
a 0
b 2
If you need additional logic to handle duplicate labels, rather than just
dropping the repeats, using groupby() on the index is a common
trick. For example, we’ll resolve duplicates by taking the average of all rows
with the same label.
In [18]: df2.groupby(level=0).mean()
Out[18]:
A
a 0.5
b 2.0
Disallowing Duplicate Labels¶
New in version 1.2.0.
As noted above, handling duplicates is an important feature when reading in raw
data. That said, you may want to avoid introducing duplicates as part of a data
processing pipeline (from methods like pandas.concat(),
rename(), etc.). Both Series and DataFrame
disallow duplicate labels by calling .set_flags(allows_duplicate_labels=False).
(the default is to allow them). If there are duplicate labels, an exception
will be raised.
In [19]: pd.Series([0, 1, 2], index=["a", "b", "b"]).set_flags(allows_duplicate_labels=False)
---------------------------------------------------------------------------
DuplicateLabelError Traceback (most recent call last)
Input In [19], in <module>
----> 1 pd.Series([0, 1, 2], index=["a", "b", "b"]).set_flags(allows_duplicate_labels=False)
File /pandas/pandas/core/generic.py:438, in NDFrame.set_flags(self, copy, allows_duplicate_labels)
436 df = self.copy(deep=copy)
437 if allows_duplicate_labels is not None:
--> 438 df.flags["allows_duplicate_labels"] = allows_duplicate_labels
439 return df
File /pandas/pandas/core/flags.py:105, in Flags.__setitem__(self, key, value)
103 if key not in self._keys:
104 raise ValueError(f"Unknown flag {key}. Must be one of {self._keys}")
--> 105 setattr(self, key, value)
File /pandas/pandas/core/flags.py:92, in Flags.allows_duplicate_labels(self, value)
90 if not value:
91 for ax in obj.axes:
---> 92 ax._maybe_check_unique()
94 self._allows_duplicate_labels = value
File /pandas/pandas/core/indexes/base.py:715, in Index._maybe_check_unique(self)
712 duplicates = self._format_duplicate_message()
713 msg += f"\n{duplicates}"
--> 715 raise DuplicateLabelError(msg)
DuplicateLabelError: Index has duplicates.
positions
label
b [1, 2]
This applies to both row and column labels for a DataFrame
In [20]: pd.DataFrame([[0, 1, 2], [3, 4, 5]], columns=["A", "B", "C"],).set_flags(
....: allows_duplicate_labels=False
....: )
....:
Out[20]:
A B C
0 0 1 2
1 3 4 5
This attribute can be checked or set with allows_duplicate_labels,
which indicates whether that object can have duplicate labels.
In [21]: df = pd.DataFrame({"A": [0, 1, 2, 3]}, index=["x", "y", "X", "Y"]).set_flags(
....: allows_duplicate_labels=False
....: )
....:
In [22]: df
Out[22]:
A
x 0
y 1
X 2
Y 3
In [23]: df.flags.allows_duplicate_labels
Out[23]: False
DataFrame.set_flags() can be used to return a new DataFrame with attributes
like allows_duplicate_labels set to some value
In [24]: df2 = df.set_flags(allows_duplicate_labels=True)
In [25]: df2.flags.allows_duplicate_labels
Out[25]: True
The new DataFrame returned is a view on the same data as the old DataFrame.
Or the property can just be set directly on the same object
In [26]: df2.flags.allows_duplicate_labels = False
In [27]: df2.flags.allows_duplicate_labels
Out[27]: False
When processing raw, messy data you might initially read in the messy data (which potentially has duplicate labels), deduplicate, and then disallow duplicates going forward, to ensure that your data pipeline doesn’t introduce duplicates.
>>> raw = pd.read_csv("...")
>>> deduplicated = raw.groupby(level=0).first() # remove duplicates
>>> deduplicated.flags.allows_duplicate_labels = False # disallow going forward
Setting allows_duplicate_labels=True on a Series or DataFrame with duplicate
labels or performing an operation that introduces duplicate labels on a Series or
DataFrame that disallows duplicates will raise an
errors.DuplicateLabelError.
In [28]: df.rename(str.upper)
---------------------------------------------------------------------------
DuplicateLabelError Traceback (most recent call last)
Input In [28], in <module>
----> 1 df.rename(str.upper)
File /pandas/pandas/core/frame.py:5077, in DataFrame.rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
4958 def rename(
4959 self,
4960 mapper: Renamer | None = None,
(...)
4968 errors: str = "ignore",
4969 ) -> DataFrame | None:
4970 """
4971 Alter axes labels.
4972
(...)
5075 4 3 6
5076 """
-> 5077 return super()._rename(
5078 mapper=mapper,
5079 index=index,
5080 columns=columns,
5081 axis=axis,
5082 copy=copy,
5083 inplace=inplace,
5084 level=level,
5085 errors=errors,
5086 )
File /pandas/pandas/core/generic.py:1171, in NDFrame._rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
1169 return None
1170 else:
-> 1171 return result.__finalize__(self, method="rename")
File /pandas/pandas/core/generic.py:5549, in NDFrame.__finalize__(self, other, method, **kwargs)
5546 for name in other.attrs:
5547 self.attrs[name] = other.attrs[name]
-> 5549 self.flags.allows_duplicate_labels = other.flags.allows_duplicate_labels
5550 # For subclasses using _metadata.
5551 for name in set(self._metadata) & set(other._metadata):
File /pandas/pandas/core/flags.py:92, in Flags.allows_duplicate_labels(self, value)
90 if not value:
91 for ax in obj.axes:
---> 92 ax._maybe_check_unique()
94 self._allows_duplicate_labels = value
File /pandas/pandas/core/indexes/base.py:715, in Index._maybe_check_unique(self)
712 duplicates = self._format_duplicate_message()
713 msg += f"\n{duplicates}"
--> 715 raise DuplicateLabelError(msg)
DuplicateLabelError: Index has duplicates.
positions
label
X [0, 2]
Y [1, 3]
This error message contains the labels that are duplicated, and the numeric positions
of all the duplicates (including the “original”) in the Series or DataFrame
Duplicate Label Propagation¶
In general, disallowing duplicates is “sticky”. It’s preserved through operations.
In [29]: s1 = pd.Series(0, index=["a", "b"]).set_flags(allows_duplicate_labels=False)
In [30]: s1
Out[30]:
a 0
b 0
dtype: int64
In [31]: s1.head().rename({"a": "b"})
---------------------------------------------------------------------------
DuplicateLabelError Traceback (most recent call last)
Input In [31], in <module>
----> 1 s1.head().rename({"a": "b"})
File /pandas/pandas/core/series.py:4601, in Series.rename(self, index, axis, copy, inplace, level, errors)
4598 axis = self._get_axis_number(axis)
4600 if callable(index) or is_dict_like(index):
-> 4601 return super()._rename(
4602 index, copy=copy, inplace=inplace, level=level, errors=errors
4603 )
4604 else:
4605 return self._set_name(index, inplace=inplace)
File /pandas/pandas/core/generic.py:1171, in NDFrame._rename(self, mapper, index, columns, axis, copy, inplace, level, errors)
1169 return None
1170 else:
-> 1171 return result.__finalize__(self, method="rename")
File /pandas/pandas/core/generic.py:5549, in NDFrame.__finalize__(self, other, method, **kwargs)
5546 for name in other.attrs:
5547 self.attrs[name] = other.attrs[name]
-> 5549 self.flags.allows_duplicate_labels = other.flags.allows_duplicate_labels
5550 # For subclasses using _metadata.
5551 for name in set(self._metadata) & set(other._metadata):
File /pandas/pandas/core/flags.py:92, in Flags.allows_duplicate_labels(self, value)
90 if not value:
91 for ax in obj.axes:
---> 92 ax._maybe_check_unique()
94 self._allows_duplicate_labels = value
File /pandas/pandas/core/indexes/base.py:715, in Index._maybe_check_unique(self)
712 duplicates = self._format_duplicate_message()
713 msg += f"\n{duplicates}"
--> 715 raise DuplicateLabelError(msg)
DuplicateLabelError: Index has duplicates.
positions
label
b [0, 1]
Warning
This is an experimental feature. Currently, many methods fail to
propagate the allows_duplicate_labels value. In future versions
it is expected that every method taking or returning one or more
DataFrame or Series objects will propagate allows_duplicate_labels.