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"""
Generic data algorithms. This module is experimental at the moment and not
intended for public consumption
"""
from __future__ import division
from warnings import warn, catch_warnings
import numpy as np
from pandas.core.dtypes.cast import maybe_promote
from pandas.core.dtypes.generic import (
ABCSeries, ABCIndex,
ABCIndexClass, ABCCategorical)
from pandas.core.dtypes.common import (
is_unsigned_integer_dtype, is_signed_integer_dtype,
is_integer_dtype, is_complex_dtype,
is_object_dtype,
is_categorical_dtype, is_sparse,
is_period_dtype,
is_numeric_dtype, is_float_dtype,
is_bool_dtype, needs_i8_conversion,
is_categorical, is_datetimetz,
is_datetime64_any_dtype, is_datetime64tz_dtype,
is_timedelta64_dtype, is_interval_dtype,
is_scalar, is_list_like,
_ensure_platform_int, _ensure_object,
_ensure_float64, _ensure_uint64,
_ensure_int64)
from pandas.compat.numpy import _np_version_under1p10
from pandas.core.dtypes.missing import isna
from pandas.core import common as com
from pandas._libs import algos, lib, hashtable as htable
from pandas._libs.tslib import iNaT
# --------------- #
# dtype access #
# --------------- #
def _ensure_data(values, dtype=None):
"""
routine to ensure that our data is of the correct
input dtype for lower-level routines
This will coerce:
- ints -> int64
- uint -> uint64
- bool -> uint64 (TODO this should be uint8)
- datetimelike -> i8
- datetime64tz -> i8 (in local tz)
- categorical -> codes
Parameters
----------
values : array-like
dtype : pandas_dtype, optional
coerce to this dtype
Returns
-------
(ndarray, pandas_dtype, algo dtype as a string)
"""
# we check some simple dtypes first
try:
if is_object_dtype(dtype):
return _ensure_object(np.asarray(values)), 'object', 'object'
if is_bool_dtype(values) or is_bool_dtype(dtype):
# we are actually coercing to uint64
# until our algos suppport uint8 directly (see TODO)
return np.asarray(values).astype('uint64'), 'bool', 'uint64'
elif is_signed_integer_dtype(values) or is_signed_integer_dtype(dtype):
return _ensure_int64(values), 'int64', 'int64'
elif (is_unsigned_integer_dtype(values) or
is_unsigned_integer_dtype(dtype)):
return _ensure_uint64(values), 'uint64', 'uint64'
elif is_float_dtype(values) or is_float_dtype(dtype):
return _ensure_float64(values), 'float64', 'float64'
elif is_object_dtype(values) and dtype is None:
return _ensure_object(np.asarray(values)), 'object', 'object'
elif is_complex_dtype(values) or is_complex_dtype(dtype):
# ignore the fact that we are casting to float
# which discards complex parts
with catch_warnings(record=True):
values = _ensure_float64(values)
return values, 'float64', 'float64'
except (TypeError, ValueError):
# if we are trying to coerce to a dtype
# and it is incompat this will fall thru to here
return _ensure_object(values), 'object', 'object'
# datetimelike
if (needs_i8_conversion(values) or
is_period_dtype(dtype) or
is_datetime64_any_dtype(dtype) or
is_timedelta64_dtype(dtype)):
if is_period_dtype(values) or is_period_dtype(dtype):
from pandas import PeriodIndex
values = PeriodIndex(values)
dtype = values.dtype
elif is_timedelta64_dtype(values) or is_timedelta64_dtype(dtype):
from pandas import TimedeltaIndex
values = TimedeltaIndex(values)
dtype = values.dtype
else:
# Datetime
from pandas import DatetimeIndex
values = DatetimeIndex(values)
dtype = values.dtype
return values.asi8, dtype, 'int64'
elif (is_categorical_dtype(values) and
(is_categorical_dtype(dtype) or dtype is None)):
values = getattr(values, 'values', values)
values = values.codes
dtype = 'category'
# we are actually coercing to int64
# until our algos suppport int* directly (not all do)
values = _ensure_int64(values)
return values, dtype, 'int64'
# we have failed, return object
values = np.asarray(values)
return _ensure_object(values), 'object', 'object'
def _reconstruct_data(values, dtype, original):
"""
reverse of _ensure_data
Parameters
----------
values : ndarray
dtype : pandas_dtype
original : ndarray-like
Returns
-------
Index for extension types, otherwise ndarray casted to dtype
"""
from pandas import Index
if is_categorical_dtype(dtype):
pass
elif is_datetime64tz_dtype(dtype) or is_period_dtype(dtype):
values = Index(original)._shallow_copy(values, name=None)
elif is_bool_dtype(dtype):
values = values.astype(dtype)
# we only support object dtypes bool Index
if isinstance(original, Index):
values = values.astype(object)
elif dtype is not None:
values = values.astype(dtype)
return values
def _ensure_arraylike(values):
"""
ensure that we are arraylike if not already
"""
if not isinstance(values, (np.ndarray, ABCCategorical,
ABCIndexClass, ABCSeries)):
inferred = lib.infer_dtype(values)
if inferred in ['mixed', 'string', 'unicode']:
if isinstance(values, tuple):
values = list(values)
values = lib.list_to_object_array(values)
else:
values = np.asarray(values)
return values
_hashtables = {
'float64': (htable.Float64HashTable, htable.Float64Vector),
'uint64': (htable.UInt64HashTable, htable.UInt64Vector),
'int64': (htable.Int64HashTable, htable.Int64Vector),
'string': (htable.StringHashTable, htable.ObjectVector),
'object': (htable.PyObjectHashTable, htable.ObjectVector)
}
def _get_hashtable_algo(values):
"""
Parameters
----------
values : arraylike
Returns
-------
tuples(hashtable class,
vector class,
values,
dtype,
ndtype)
"""
values, dtype, ndtype = _ensure_data(values)
if ndtype == 'object':
# its cheaper to use a String Hash Table than Object
if lib.infer_dtype(values) in ['string']:
ndtype = 'string'
else:
ndtype = 'object'
htable, table = _hashtables[ndtype]
return (htable, table, values, dtype, ndtype)
def _get_data_algo(values, func_map):
if is_categorical_dtype(values):
values = values._values_for_rank()
values, dtype, ndtype = _ensure_data(values)
if ndtype == 'object':
# its cheaper to use a String Hash Table than Object
if lib.infer_dtype(values) in ['string']:
ndtype = 'string'
f = func_map.get(ndtype, func_map['object'])
return f, values
# --------------- #
# top-level algos #
# --------------- #
def match(to_match, values, na_sentinel=-1):
"""
Compute locations of to_match into values
Parameters
----------
to_match : array-like
values to find positions of
values : array-like
Unique set of values
na_sentinel : int, default -1
Value to mark "not found"
Examples
--------
Returns
-------
match : ndarray of integers
"""
values = com._asarray_tuplesafe(values)
htable, _, values, dtype, ndtype = _get_hashtable_algo(values)
to_match, _, _ = _ensure_data(to_match, dtype)
table = htable(min(len(to_match), 1000000))
table.map_locations(values)
result = table.lookup(to_match)
if na_sentinel != -1:
# replace but return a numpy array
# use a Series because it handles dtype conversions properly
from pandas import Series
result = Series(result.ravel()).replace(-1, na_sentinel).values.\
reshape(result.shape)
return result
def unique(values):
"""
Hash table-based unique. Uniques are returned in order
of appearance. This does NOT sort.
Significantly faster than numpy.unique. Includes NA values.
Parameters
----------
values : 1d array-like
Returns
-------
unique values.
- If the input is an Index, the return is an Index
- If the input is a Categorical dtype, the return is a Categorical
- If the input is a Series/ndarray, the return will be an ndarray
Examples
--------
>>> pd.unique(pd.Series([2, 1, 3, 3]))
array([2, 1, 3])
>>> pd.unique(pd.Series([2] + [1] * 5))
array([2, 1])
>>> pd.unique(Series([pd.Timestamp('20160101'),
... pd.Timestamp('20160101')]))
array(['2016-01-01T00:00:00.000000000'], dtype='datetime64[ns]')
>>> pd.unique(pd.Series([pd.Timestamp('20160101', tz='US/Eastern'),
... pd.Timestamp('20160101', tz='US/Eastern')]))
array([Timestamp('2016-01-01 00:00:00-0500', tz='US/Eastern')],
dtype=object)
>>> pd.unique(pd.Index([pd.Timestamp('20160101', tz='US/Eastern'),
... pd.Timestamp('20160101', tz='US/Eastern')]))
DatetimeIndex(['2016-01-01 00:00:00-05:00'],
... dtype='datetime64[ns, US/Eastern]', freq=None)
>>> pd.unique(list('baabc'))
array(['b', 'a', 'c'], dtype=object)
An unordered Categorical will return categories in the
order of appearance.
>>> pd.unique(Series(pd.Categorical(list('baabc'))))
[b, a, c]
Categories (3, object): [b, a, c]
>>> pd.unique(Series(pd.Categorical(list('baabc'),
... categories=list('abc'))))
[b, a, c]
Categories (3, object): [b, a, c]
An ordered Categorical preserves the category ordering.
>>> pd.unique(Series(pd.Categorical(list('baabc'),
... categories=list('abc'),
... ordered=True)))
[b, a, c]
Categories (3, object): [a < b < c]
An array of tuples
>>> pd.unique([('a', 'b'), ('b', 'a'), ('a', 'c'), ('b', 'a')])
array([('a', 'b'), ('b', 'a'), ('a', 'c')], dtype=object)
See Also
--------
pandas.Index.unique
pandas.Series.unique
"""
values = _ensure_arraylike(values)
# categorical is a fast-path
# this will coerce Categorical, CategoricalIndex,
# and category dtypes Series to same return of Category
if is_categorical_dtype(values):
values = getattr(values, '.values', values)
return values.unique()
original = values
htable, _, values, dtype, ndtype = _get_hashtable_algo(values)
table = htable(len(values))
uniques = table.unique(values)
uniques = _reconstruct_data(uniques, dtype, original)
if isinstance(original, ABCSeries) and is_datetime64tz_dtype(dtype):
# we are special casing datetime64tz_dtype
# to return an object array of tz-aware Timestamps
# TODO: it must return DatetimeArray with tz in pandas 2.0
uniques = uniques.asobject.values
return uniques
unique1d = unique
def isin(comps, values):
"""
Compute the isin boolean array
Parameters
----------
comps: array-like
values: array-like
Returns
-------
boolean array same length as comps
"""
if not is_list_like(comps):
raise TypeError("only list-like objects are allowed to be passed"
" to isin(), you passed a [{comps_type}]"
.format(comps_type=type(comps).__name__))
if not is_list_like(values):
raise TypeError("only list-like objects are allowed to be passed"
" to isin(), you passed a [{values_type}]"
.format(values_type=type(values).__name__))
if not isinstance(values, (ABCIndex, ABCSeries, np.ndarray)):
values = lib.list_to_object_array(list(values))
comps, dtype, _ = _ensure_data(comps)
values, _, _ = _ensure_data(values, dtype=dtype)
# faster for larger cases to use np.in1d
f = lambda x, y: htable.ismember_object(x, values)
# GH16012
# Ensure np.in1d doesn't get object types or it *may* throw an exception
if len(comps) > 1000000 and not is_object_dtype(comps):
f = lambda x, y: np.in1d(x, y)
elif is_integer_dtype(comps):
try:
values = values.astype('int64', copy=False)
comps = comps.astype('int64', copy=False)
f = lambda x, y: htable.ismember_int64(x, y)
except (TypeError, ValueError):
values = values.astype(object)
comps = comps.astype(object)
elif is_float_dtype(comps):
try:
values = values.astype('float64', copy=False)
comps = comps.astype('float64', copy=False)
checknull = isna(values).any()
f = lambda x, y: htable.ismember_float64(x, y, checknull)
except (TypeError, ValueError):
values = values.astype(object)
comps = comps.astype(object)
return f(comps, values)
def factorize(values, sort=False, order=None, na_sentinel=-1, size_hint=None):
"""
Encode input values as an enumerated type or categorical variable
Parameters
----------
values : ndarray (1-d)
Sequence
sort : boolean, default False
Sort by values
na_sentinel : int, default -1
Value to mark "not found"
size_hint : hint to the hashtable sizer
Returns
-------
labels : the indexer to the original array
uniques : ndarray (1-d) or Index
the unique values. Index is returned when passed values is Index or
Series
note: an array of Periods will ignore sort as it returns an always sorted
PeriodIndex
"""
values = _ensure_arraylike(values)
original = values
values, dtype, _ = _ensure_data(values)
(hash_klass, vec_klass), values = _get_data_algo(values, _hashtables)
table = hash_klass(size_hint or len(values))
uniques = vec_klass()
check_nulls = not is_integer_dtype(original)
labels = table.get_labels(values, uniques, 0, na_sentinel, check_nulls)
labels = _ensure_platform_int(labels)
uniques = uniques.to_array()
if sort and len(uniques) > 0:
from pandas.core.sorting import safe_sort
uniques, labels = safe_sort(uniques, labels, na_sentinel=na_sentinel,
assume_unique=True)
uniques = _reconstruct_data(uniques, dtype, original)
# return original tenor
if isinstance(original, ABCIndexClass):
uniques = original._shallow_copy(uniques, name=None)
elif isinstance(original, ABCSeries):
from pandas import Index
uniques = Index(uniques)
return labels, uniques
def value_counts(values, sort=True, ascending=False, normalize=False,
bins=None, dropna=True):
"""
Compute a histogram of the counts of non-null values.
Parameters
----------
values : ndarray (1-d)
sort : boolean, default True
Sort by values
ascending : boolean, default False
Sort in ascending order
normalize: boolean, default False
If True then compute a relative histogram
bins : integer, optional
Rather than count values, group them into half-open bins,
convenience for pd.cut, only works with numeric data
dropna : boolean, default True
Don't include counts of NaN
Returns
-------
value_counts : Series
"""
from pandas.core.series import Series, Index
name = getattr(values, 'name', None)
if bins is not None:
try:
from pandas.core.reshape.tile import cut
values = Series(values)
ii = cut(values, bins, include_lowest=True)
except TypeError:
raise TypeError("bins argument only works with numeric data.")
# count, remove nulls (from the index), and but the bins
result = ii.value_counts(dropna=dropna)
result = result[result.index.notna()]
result.index = result.index.astype('interval')
result = result.sort_index()
# if we are dropna and we have NO values
if dropna and (result.values == 0).all():
result = result.iloc[0:0]
# normalizing is by len of all (regardless of dropna)
counts = np.array([len(ii)])
else:
if is_categorical_dtype(values) or is_sparse(values):
# handle Categorical and sparse,
result = Series(values).values.value_counts(dropna=dropna)
result.name = name
counts = result.values
else:
keys, counts = _value_counts_arraylike(values, dropna)
if not isinstance(keys, Index):
keys = Index(keys)
result = Series(counts, index=keys, name=name)
if sort:
result = result.sort_values(ascending=ascending)
if normalize:
result = result / float(counts.sum())
return result
def _value_counts_arraylike(values, dropna):
"""
Parameters
----------
values : arraylike
dropna : boolean
Returns
-------
(uniques, counts)
"""
values = _ensure_arraylike(values)
original = values
values, dtype, ndtype = _ensure_data(values)
if needs_i8_conversion(dtype):
# i8
keys, counts = htable.value_count_int64(values, dropna)
if dropna:
msk = keys != iNaT
keys, counts = keys[msk], counts[msk]
else:
# ndarray like
# TODO: handle uint8
f = getattr(htable, "value_count_{dtype}".format(dtype=ndtype))
keys, counts = f(values, dropna)
mask = isna(values)
if not dropna and mask.any():
if not isna(keys).any():
keys = np.insert(keys, 0, np.NaN)
counts = np.insert(counts, 0, mask.sum())
keys = _reconstruct_data(keys, original.dtype, original)
return keys, counts
def duplicated(values, keep='first'):
"""
Return boolean ndarray denoting duplicate values.
.. versionadded:: 0.19.0
Parameters
----------
values : ndarray-like
Array over which to check for duplicate values.
keep : {'first', 'last', False}, default 'first'
- ``first`` : Mark duplicates as ``True`` except for the first
occurrence.
- ``last`` : Mark duplicates as ``True`` except for the last
occurrence.
- False : Mark all duplicates as ``True``.
Returns
-------
duplicated : ndarray
"""
values, dtype, ndtype = _ensure_data(values)
f = getattr(htable, "duplicated_{dtype}".format(dtype=ndtype))
return f(values, keep=keep)
def mode(values):
"""
Returns the mode(s) of an array.
Parameters
----------
values : array-like
Array over which to check for duplicate values.
Returns
-------
mode : Series
"""
from pandas import Series
values = _ensure_arraylike(values)
original = values
# categorical is a fast-path
if is_categorical_dtype(values):
if isinstance(values, Series):
return Series(values.values.mode(), name=values.name)
return values.mode()
values, dtype, ndtype = _ensure_data(values)
# TODO: this should support float64
if ndtype not in ['int64', 'uint64', 'object']:
ndtype = 'object'
values = _ensure_object(values)
f = getattr(htable, "mode_{dtype}".format(dtype=ndtype))
result = f(values)
try:
result = np.sort(result)
except TypeError as e:
warn("Unable to sort modes: {error}".format(error=e))
result = _reconstruct_data(result, original.dtype, original)
return Series(result)
def rank(values, axis=0, method='average', na_option='keep',
ascending=True, pct=False):
"""
Rank the values along a given axis.
Parameters
----------
values : array-like
Array whose values will be ranked. The number of dimensions in this
array must not exceed 2.
axis : int, default 0
Axis over which to perform rankings.
method : {'average', 'min', 'max', 'first', 'dense'}, default 'average'
The method by which tiebreaks are broken during the ranking.
na_option : {'keep', 'top'}, default 'keep'
The method by which NaNs are placed in the ranking.
- ``keep``: rank each NaN value with a NaN ranking
- ``top``: replace each NaN with either +/- inf so that they
there are ranked at the top
ascending : boolean, default True
Whether or not the elements should be ranked in ascending order.
pct : boolean, default False
Whether or not to the display the returned rankings in integer form
(e.g. 1, 2, 3) or in percentile form (e.g. 0.333..., 0.666..., 1).
"""
if values.ndim == 1:
f, values = _get_data_algo(values, _rank1d_functions)
ranks = f(values, ties_method=method, ascending=ascending,
na_option=na_option, pct=pct)
elif values.ndim == 2:
f, values = _get_data_algo(values, _rank2d_functions)
ranks = f(values, axis=axis, ties_method=method,
ascending=ascending, na_option=na_option, pct=pct)
else:
raise TypeError("Array with ndim > 2 are not supported.")
return ranks
def checked_add_with_arr(arr, b, arr_mask=None, b_mask=None):
"""
Perform array addition that checks for underflow and overflow.
Performs the addition of an int64 array and an int64 integer (or array)
but checks that they do not result in overflow first. For elements that
are indicated to be NaN, whether or not there is overflow for that element
is automatically ignored.
Parameters
----------
arr : array addend.
b : array or scalar addend.
arr_mask : boolean array or None
array indicating which elements to exclude from checking
b_mask : boolean array or boolean or None
array or scalar indicating which element(s) to exclude from checking
Returns
-------
sum : An array for elements x + b for each element x in arr if b is
a scalar or an array for elements x + y for each element pair
(x, y) in (arr, b).
Raises
------
OverflowError if any x + y exceeds the maximum or minimum int64 value.
"""
def _broadcast(arr_or_scalar, shape):
"""
Helper function to broadcast arrays / scalars to the desired shape.
"""
if _np_version_under1p10:
if lib.isscalar(arr_or_scalar):
out = np.empty(shape)
out.fill(arr_or_scalar)
else:
out = arr_or_scalar
else:
out = np.broadcast_to(arr_or_scalar, shape)
return out
# For performance reasons, we broadcast 'b' to the new array 'b2'
# so that it has the same size as 'arr'.
b2 = _broadcast(b, arr.shape)
if b_mask is not None:
# We do the same broadcasting for b_mask as well.
b2_mask = _broadcast(b_mask, arr.shape)
else:
b2_mask = None
# For elements that are NaN, regardless of their value, we should
# ignore whether they overflow or not when doing the checked add.
if arr_mask is not None and b2_mask is not None:
not_nan = np.logical_not(arr_mask | b2_mask)
elif arr_mask is not None:
not_nan = np.logical_not(arr_mask)
elif b_mask is not None:
not_nan = np.logical_not(b2_mask)
else:
not_nan = np.empty(arr.shape, dtype=bool)
not_nan.fill(True)
# gh-14324: For each element in 'arr' and its corresponding element
# in 'b2', we check the sign of the element in 'b2'. If it is positive,
# we then check whether its sum with the element in 'arr' exceeds
# np.iinfo(np.int64).max. If so, we have an overflow error. If it
# it is negative, we then check whether its sum with the element in
# 'arr' exceeds np.iinfo(np.int64).min. If so, we have an overflow
# error as well.
mask1 = b2 > 0
mask2 = b2 < 0
if not mask1.any():
to_raise = ((np.iinfo(np.int64).min - b2 > arr) & not_nan).any()
elif not mask2.any():
to_raise = ((np.iinfo(np.int64).max - b2 < arr) & not_nan).any()
else:
to_raise = (((np.iinfo(np.int64).max -
b2[mask1] < arr[mask1]) & not_nan[mask1]).any() or
((np.iinfo(np.int64).min -
b2[mask2] > arr[mask2]) & not_nan[mask2]).any())
if to_raise:
raise OverflowError("Overflow in int64 addition")
return arr + b
_rank1d_functions = {
'float64': algos.rank_1d_float64,
'int64': algos.rank_1d_int64,
'uint64': algos.rank_1d_uint64,
'object': algos.rank_1d_object
}
_rank2d_functions = {
'float64': algos.rank_2d_float64,
'int64': algos.rank_2d_int64,
'uint64': algos.rank_2d_uint64,
'object': algos.rank_2d_object
}
def quantile(x, q, interpolation_method='fraction'):
"""
Compute sample quantile or quantiles of the input array. For example, q=0.5
computes the median.
The `interpolation_method` parameter supports three values, namely
`fraction` (default), `lower` and `higher`. Interpolation is done only,
if the desired quantile lies between two data points `i` and `j`. For
`fraction`, the result is an interpolated value between `i` and `j`;
for `lower`, the result is `i`, for `higher` the result is `j`.
Parameters
----------
x : ndarray
Values from which to extract score.
q : scalar or array
Percentile at which to extract score.
interpolation_method : {'fraction', 'lower', 'higher'}, optional
This optional parameter specifies the interpolation method to use,
when the desired quantile lies between two data points `i` and `j`:
- fraction: `i + (j - i)*fraction`, where `fraction` is the
fractional part of the index surrounded by `i` and `j`.
-lower: `i`.
- higher: `j`.
Returns
-------
score : float
Score at percentile.
Examples
--------
>>> from scipy import stats
>>> a = np.arange(100)
>>> stats.scoreatpercentile(a, 50)
49.5
"""
x = np.asarray(x)
mask = isna(x)
x = x[~mask]
values = np.sort(x)
def _interpolate(a, b, fraction):
"""Returns the point at the given fraction between a and b, where
'fraction' must be between 0 and 1.
"""
return a + (b - a) * fraction
def _get_score(at):
if len(values) == 0:
return np.nan
idx = at * (len(values) - 1)
if idx % 1 == 0:
score = values[int(idx)]
else:
if interpolation_method == 'fraction':
score = _interpolate(values[int(idx)], values[int(idx) + 1],
idx % 1)
elif interpolation_method == 'lower':
score = values[np.floor(idx)]
elif interpolation_method == 'higher':
score = values[np.ceil(idx)]
else:
raise ValueError("interpolation_method can only be 'fraction' "
", 'lower' or 'higher'")
return score
if is_scalar(q):
return _get_score(q)
else:
q = np.asarray(q, np.float64)
return algos.arrmap_float64(q, _get_score)
# --------------- #
# select n #
# --------------- #
class SelectN(object):
def __init__(self, obj, n, keep):
self.obj = obj
self.n = n
self.keep = keep
if self.keep not in ('first', 'last'):
raise ValueError('keep must be either "first", "last"')
def nlargest(self):
return self.compute('nlargest')
def nsmallest(self):
return self.compute('nsmallest')
@staticmethod
def is_valid_dtype_n_method(dtype):
"""
Helper function to determine if dtype is valid for
nsmallest/nlargest methods
"""
return ((is_numeric_dtype(dtype) and not is_complex_dtype(dtype)) or
needs_i8_conversion(dtype))
class SelectNSeries(SelectN):
"""
Implement n largest/smallest for Series
Parameters
----------
obj : Series
n : int
keep : {'first', 'last'}, default 'first'
Returns
-------
nordered : Series
"""
def compute(self, method):
n = self.n
dtype = self.obj.dtype
if not self.is_valid_dtype_n_method(dtype):
raise TypeError("Cannot use method '{method}' with "
"dtype {dtype}".format(method=method,
dtype=dtype))
if n <= 0:
return self.obj[[]]
dropped = self.obj.dropna()
# slow method
if n >= len(self.obj):
reverse_it = (self.keep == 'last' or method == 'nlargest')
ascending = method == 'nsmallest'
slc = np.s_[::-1] if reverse_it else np.s_[:]
return dropped[slc].sort_values(ascending=ascending).head(n)
# fast method
arr, _, _ = _ensure_data(dropped.values)
if method == 'nlargest':
arr = -arr
if self.keep == 'last':
arr = arr[::-1]
narr = len(arr)
n = min(n, narr)
kth_val = algos.kth_smallest(arr.copy(), n - 1)
ns, = np.nonzero(arr <= kth_val)
inds = ns[arr[ns].argsort(kind='mergesort')][:n]
if self.keep == 'last':
# reverse indices
inds = narr - 1 - inds
return dropped.iloc[inds]
class SelectNFrame(SelectN):
"""
Implement n largest/smallest for DataFrame
Parameters
----------
obj : DataFrame
n : int
keep : {'first', 'last'}, default 'first'
columns : list or str
Returns
-------
nordered : DataFrame
"""
def __init__(self, obj, n, keep, columns):
super(SelectNFrame, self).__init__(obj, n, keep)
if not is_list_like(columns):
columns = [columns]
columns = list(columns)
self.columns = columns
def compute(self, method):
from pandas import Int64Index
n = self.n
frame = self.obj
columns = self.columns
for column in columns:
dtype = frame[column].dtype
if not self.is_valid_dtype_n_method(dtype):
raise TypeError((
"Column {column!r} has dtype {dtype}, cannot use method "
"{method!r} with this dtype"
).format(column=column, dtype=dtype, method=method))
def get_indexer(current_indexer, other_indexer):
"""Helper function to concat `current_indexer` and `other_indexer`
depending on `method`
"""
if method == 'nsmallest':
return current_indexer.append(other_indexer)
else:
return other_indexer.append(current_indexer)
# Below we save and reset the index in case index contains duplicates
original_index = frame.index
cur_frame = frame = frame.reset_index(drop=True)
cur_n = n
indexer = Int64Index([])
for i, column in enumerate(columns):
# For each column we apply method to cur_frame[column].
# If it is the last column in columns, or if the values
# returned are unique in frame[column] we save this index
# and break
# Otherwise we must save the index of the non duplicated values
# and set the next cur_frame to cur_frame filtered on all
# duplcicated values (#GH15297)
series = cur_frame[column]
values = getattr(series, method)(cur_n, keep=self.keep)
is_last_column = len(columns) - 1 == i
if is_last_column or values.nunique() == series.isin(values).sum():
# Last column in columns or values are unique in
# series => values
# is all that matters
indexer = get_indexer(indexer, values.index)
break
duplicated_filter = series.duplicated(keep=False)
duplicated = values[duplicated_filter]
non_duplicated = values[~duplicated_filter]
indexer = get_indexer(indexer, non_duplicated.index)
# Must set cur frame to include all duplicated values
# to consider for the next column, we also can reduce
# cur_n by the current length of the indexer
cur_frame = cur_frame[series.isin(duplicated)]
cur_n = n - len(indexer)
frame = frame.take(indexer)
# Restore the index on frame
frame.index = original_index.take(indexer)
return frame
# ------- ## ---- #
# take #
# ---- #
def _view_wrapper(f, arr_dtype=None, out_dtype=None, fill_wrap=None):
def wrapper(arr, indexer, out, fill_value=np.nan):
if arr_dtype is not None:
arr = arr.view(arr_dtype)
if out_dtype is not None:
out = out.view(out_dtype)
if fill_wrap is not None:
fill_value = fill_wrap(fill_value)
f(arr, indexer, out, fill_value=fill_value)
return wrapper
def _convert_wrapper(f, conv_dtype):
def wrapper(arr, indexer, out, fill_value=np.nan):
arr = arr.astype(conv_dtype)
f(arr, indexer, out, fill_value=fill_value)
return wrapper
def _take_2d_multi_object(arr, indexer, out, fill_value, mask_info):
# this is not ideal, performance-wise, but it's better than raising
# an exception (best to optimize in Cython to avoid getting here)
row_idx, col_idx = indexer
if mask_info is not None:
(row_mask, col_mask), (row_needs, col_needs) = mask_info
else:
row_mask = row_idx == -1
col_mask = col_idx == -1
row_needs = row_mask.any()
col_needs = col_mask.any()
if fill_value is not None:
if row_needs:
out[row_mask, :] = fill_value
if col_needs:
out[:, col_mask] = fill_value
for i in range(len(row_idx)):
u_ = row_idx[i]
for j in range(len(col_idx)):
v = col_idx[j]
out[i, j] = arr[u_, v]
def _take_nd_object(arr, indexer, out, axis, fill_value, mask_info):
if mask_info is not None:
mask, needs_masking = mask_info
else:
mask = indexer == -1
needs_masking = mask.any()
if arr.dtype != out.dtype:
arr = arr.astype(out.dtype)
if arr.shape[axis] > 0:
arr.take(_ensure_platform_int(indexer), axis=axis, out=out)
if needs_masking:
outindexer = [slice(None)] * arr.ndim
outindexer[axis] = mask
out[tuple(outindexer)] = fill_value
_take_1d_dict = {
('int8', 'int8'): algos.take_1d_int8_int8,
('int8', 'int32'): algos.take_1d_int8_int32,
('int8', 'int64'): algos.take_1d_int8_int64,
('int8', 'float64'): algos.take_1d_int8_float64,
('int16', 'int16'): algos.take_1d_int16_int16,
('int16', 'int32'): algos.take_1d_int16_int32,
('int16', 'int64'): algos.take_1d_int16_int64,
('int16', 'float64'): algos.take_1d_int16_float64,
('int32', 'int32'): algos.take_1d_int32_int32,
('int32', 'int64'): algos.take_1d_int32_int64,
('int32', 'float64'): algos.take_1d_int32_float64,
('int64', 'int64'): algos.take_1d_int64_int64,
('int64', 'float64'): algos.take_1d_int64_float64,
('float32', 'float32'): algos.take_1d_float32_float32,
('float32', 'float64'): algos.take_1d_float32_float64,
('float64', 'float64'): algos.take_1d_float64_float64,
('object', 'object'): algos.take_1d_object_object,
('bool', 'bool'): _view_wrapper(algos.take_1d_bool_bool, np.uint8,
np.uint8),
('bool', 'object'): _view_wrapper(algos.take_1d_bool_object, np.uint8,
None),
('datetime64[ns]', 'datetime64[ns]'): _view_wrapper(
algos.take_1d_int64_int64, np.int64, np.int64, np.int64)
}
_take_2d_axis0_dict = {
('int8', 'int8'): algos.take_2d_axis0_int8_int8,
('int8', 'int32'): algos.take_2d_axis0_int8_int32,
('int8', 'int64'): algos.take_2d_axis0_int8_int64,
('int8', 'float64'): algos.take_2d_axis0_int8_float64,
('int16', 'int16'): algos.take_2d_axis0_int16_int16,
('int16', 'int32'): algos.take_2d_axis0_int16_int32,
('int16', 'int64'): algos.take_2d_axis0_int16_int64,
('int16', 'float64'): algos.take_2d_axis0_int16_float64,
('int32', 'int32'): algos.take_2d_axis0_int32_int32,
('int32', 'int64'): algos.take_2d_axis0_int32_int64,
('int32', 'float64'): algos.take_2d_axis0_int32_float64,
('int64', 'int64'): algos.take_2d_axis0_int64_int64,
('int64', 'float64'): algos.take_2d_axis0_int64_float64,
('float32', 'float32'): algos.take_2d_axis0_float32_float32,
('float32', 'float64'): algos.take_2d_axis0_float32_float64,
('float64', 'float64'): algos.take_2d_axis0_float64_float64,
('object', 'object'): algos.take_2d_axis0_object_object,
('bool', 'bool'): _view_wrapper(algos.take_2d_axis0_bool_bool, np.uint8,
np.uint8),
('bool', 'object'): _view_wrapper(algos.take_2d_axis0_bool_object,
np.uint8, None),
('datetime64[ns]', 'datetime64[ns]'):
_view_wrapper(algos.take_2d_axis0_int64_int64, np.int64, np.int64,
fill_wrap=np.int64)
}
_take_2d_axis1_dict = {
('int8', 'int8'): algos.take_2d_axis1_int8_int8,
('int8', 'int32'): algos.take_2d_axis1_int8_int32,
('int8', 'int64'): algos.take_2d_axis1_int8_int64,
('int8', 'float64'): algos.take_2d_axis1_int8_float64,
('int16', 'int16'): algos.take_2d_axis1_int16_int16,
('int16', 'int32'): algos.take_2d_axis1_int16_int32,
('int16', 'int64'): algos.take_2d_axis1_int16_int64,
('int16', 'float64'): algos.take_2d_axis1_int16_float64,
('int32', 'int32'): algos.take_2d_axis1_int32_int32,
('int32', 'int64'): algos.take_2d_axis1_int32_int64,
('int32', 'float64'): algos.take_2d_axis1_int32_float64,
('int64', 'int64'): algos.take_2d_axis1_int64_int64,
('int64', 'float64'): algos.take_2d_axis1_int64_float64,
('float32', 'float32'): algos.take_2d_axis1_float32_float32,
('float32', 'float64'): algos.take_2d_axis1_float32_float64,
('float64', 'float64'): algos.take_2d_axis1_float64_float64,
('object', 'object'): algos.take_2d_axis1_object_object,
('bool', 'bool'): _view_wrapper(algos.take_2d_axis1_bool_bool, np.uint8,
np.uint8),
('bool', 'object'): _view_wrapper(algos.take_2d_axis1_bool_object,
np.uint8, None),
('datetime64[ns]', 'datetime64[ns]'):
_view_wrapper(algos.take_2d_axis1_int64_int64, np.int64, np.int64,
fill_wrap=np.int64)
}
_take_2d_multi_dict = {
('int8', 'int8'): algos.take_2d_multi_int8_int8,
('int8', 'int32'): algos.take_2d_multi_int8_int32,
('int8', 'int64'): algos.take_2d_multi_int8_int64,
('int8', 'float64'): algos.take_2d_multi_int8_float64,
('int16', 'int16'): algos.take_2d_multi_int16_int16,
('int16', 'int32'): algos.take_2d_multi_int16_int32,
('int16', 'int64'): algos.take_2d_multi_int16_int64,
('int16', 'float64'): algos.take_2d_multi_int16_float64,
('int32', 'int32'): algos.take_2d_multi_int32_int32,
('int32', 'int64'): algos.take_2d_multi_int32_int64,
('int32', 'float64'): algos.take_2d_multi_int32_float64,
('int64', 'int64'): algos.take_2d_multi_int64_int64,
('int64', 'float64'): algos.take_2d_multi_int64_float64,
('float32', 'float32'): algos.take_2d_multi_float32_float32,
('float32', 'float64'): algos.take_2d_multi_float32_float64,
('float64', 'float64'): algos.take_2d_multi_float64_float64,
('object', 'object'): algos.take_2d_multi_object_object,
('bool', 'bool'): _view_wrapper(algos.take_2d_multi_bool_bool, np.uint8,
np.uint8),
('bool', 'object'): _view_wrapper(algos.take_2d_multi_bool_object,
np.uint8, None),
('datetime64[ns]', 'datetime64[ns]'):
_view_wrapper(algos.take_2d_multi_int64_int64, np.int64, np.int64,
fill_wrap=np.int64)
}
def _get_take_nd_function(ndim, arr_dtype, out_dtype, axis=0, mask_info=None):
if ndim <= 2:
tup = (arr_dtype.name, out_dtype.name)
if ndim == 1:
func = _take_1d_dict.get(tup, None)
elif ndim == 2:
if axis == 0:
func = _take_2d_axis0_dict.get(tup, None)
else:
func = _take_2d_axis1_dict.get(tup, None)
if func is not None:
return func
tup = (out_dtype.name, out_dtype.name)
if ndim == 1:
func = _take_1d_dict.get(tup, None)
elif ndim == 2:
if axis == 0:
func = _take_2d_axis0_dict.get(tup, None)
else:
func = _take_2d_axis1_dict.get(tup, None)
if func is not None:
func = _convert_wrapper(func, out_dtype)
return func
def func(arr, indexer, out, fill_value=np.nan):
indexer = _ensure_int64(indexer)
_take_nd_object(arr, indexer, out, axis=axis, fill_value=fill_value,
mask_info=mask_info)
return func
def take_nd(arr, indexer, axis=0, out=None, fill_value=np.nan, mask_info=None,
allow_fill=True):
"""
Specialized Cython take which sets NaN values in one pass
Parameters
----------
arr : ndarray
Input array
indexer : ndarray
1-D array of indices to take, subarrays corresponding to -1 value
indicies are filed with fill_value
axis : int, default 0
Axis to take from
out : ndarray or None, default None
Optional output array, must be appropriate type to hold input and
fill_value together, if indexer has any -1 value entries; call
_maybe_promote to determine this type for any fill_value
fill_value : any, default np.nan
Fill value to replace -1 values with
mask_info : tuple of (ndarray, boolean)
If provided, value should correspond to:
(indexer != -1, (indexer != -1).any())
If not provided, it will be computed internally if necessary
allow_fill : boolean, default True
If False, indexer is assumed to contain no -1 values so no filling
will be done. This short-circuits computation of a mask. Result is
undefined if allow_fill == False and -1 is present in indexer.
"""
# dispatch to internal type takes
if is_categorical(arr):
return arr.take_nd(indexer, fill_value=fill_value,
allow_fill=allow_fill)
elif is_datetimetz(arr):
return arr.take(indexer, fill_value=fill_value, allow_fill=allow_fill)
elif is_interval_dtype(arr):
return arr.take(indexer, fill_value=fill_value, allow_fill=allow_fill)
if indexer is None:
indexer = np.arange(arr.shape[axis], dtype=np.int64)
dtype, fill_value = arr.dtype, arr.dtype.type()
else:
indexer = _ensure_int64(indexer, copy=False)
if not allow_fill:
dtype, fill_value = arr.dtype, arr.dtype.type()
mask_info = None, False
else:
# check for promotion based on types only (do this first because
# it's faster than computing a mask)
dtype, fill_value = maybe_promote(arr.dtype, fill_value)
if dtype != arr.dtype and (out is None or out.dtype != dtype):
# check if promotion is actually required based on indexer
if mask_info is not None:
mask, needs_masking = mask_info
else:
mask = indexer == -1
needs_masking = mask.any()
mask_info = mask, needs_masking
if needs_masking:
if out is not None and out.dtype != dtype:
raise TypeError('Incompatible type for fill_value')
else:
# if not, then depromote, set fill_value to dummy
# (it won't be used but we don't want the cython code
# to crash when trying to cast it to dtype)
dtype, fill_value = arr.dtype, arr.dtype.type()
flip_order = False
if arr.ndim == 2:
if arr.flags.f_contiguous:
flip_order = True
if flip_order:
arr = arr.T
axis = arr.ndim - axis - 1
if out is not None:
out = out.T
# at this point, it's guaranteed that dtype can hold both the arr values
# and the fill_value
if out is None:
out_shape = list(arr.shape)
out_shape[axis] = len(indexer)
out_shape = tuple(out_shape)
if arr.flags.f_contiguous and axis == arr.ndim - 1:
# minor tweak that can make an order-of-magnitude difference
# for dataframes initialized directly from 2-d ndarrays
# (s.t. df.values is c-contiguous and df._data.blocks[0] is its
# f-contiguous transpose)
out = np.empty(out_shape, dtype=dtype, order='F')
else:
out = np.empty(out_shape, dtype=dtype)
func = _get_take_nd_function(arr.ndim, arr.dtype, out.dtype, axis=axis,
mask_info=mask_info)
func(arr, indexer, out, fill_value)
if flip_order:
out = out.T
return out
take_1d = take_nd
def take_2d_multi(arr, indexer, out=None, fill_value=np.nan, mask_info=None,
allow_fill=True):
"""
Specialized Cython take which sets NaN values in one pass
"""
if indexer is None or (indexer[0] is None and indexer[1] is None):
row_idx = np.arange(arr.shape[0], dtype=np.int64)
col_idx = np.arange(arr.shape[1], dtype=np.int64)
indexer = row_idx, col_idx
dtype, fill_value = arr.dtype, arr.dtype.type()
else:
row_idx, col_idx = indexer
if row_idx is None:
row_idx = np.arange(arr.shape[0], dtype=np.int64)
else:
row_idx = _ensure_int64(row_idx)
if col_idx is None:
col_idx = np.arange(arr.shape[1], dtype=np.int64)
else:
col_idx = _ensure_int64(col_idx)
indexer = row_idx, col_idx
if not allow_fill:
dtype, fill_value = arr.dtype, arr.dtype.type()
mask_info = None, False
else:
# check for promotion based on types only (do this first because
# it's faster than computing a mask)
dtype, fill_value = maybe_promote(arr.dtype, fill_value)
if dtype != arr.dtype and (out is None or out.dtype != dtype):
# check if promotion is actually required based on indexer
if mask_info is not None:
(row_mask, col_mask), (row_needs, col_needs) = mask_info
else:
row_mask = row_idx == -1
col_mask = col_idx == -1
row_needs = row_mask.any()
col_needs = col_mask.any()
mask_info = (row_mask, col_mask), (row_needs, col_needs)
if row_needs or col_needs:
if out is not None and out.dtype != dtype:
raise TypeError('Incompatible type for fill_value')
else:
# if not, then depromote, set fill_value to dummy
# (it won't be used but we don't want the cython code
# to crash when trying to cast it to dtype)
dtype, fill_value = arr.dtype, arr.dtype.type()
# at this point, it's guaranteed that dtype can hold both the arr values
# and the fill_value
if out is None:
out_shape = len(row_idx), len(col_idx)
out = np.empty(out_shape, dtype=dtype)
func = _take_2d_multi_dict.get((arr.dtype.name, out.dtype.name), None)
if func is None and arr.dtype != out.dtype:
func = _take_2d_multi_dict.get((out.dtype.name, out.dtype.name), None)
if func is not None:
func = _convert_wrapper(func, out.dtype)
if func is None:
def func(arr, indexer, out, fill_value=np.nan):
_take_2d_multi_object(arr, indexer, out, fill_value=fill_value,
mask_info=mask_info)
func(arr, indexer, out=out, fill_value=fill_value)
return out
# ---- #
# diff #
# ---- #
_diff_special = {
'float64': algos.diff_2d_float64,
'float32': algos.diff_2d_float32,
'int64': algos.diff_2d_int64,
'int32': algos.diff_2d_int32,
'int16': algos.diff_2d_int16,
'int8': algos.diff_2d_int8,
}
def diff(arr, n, axis=0):
"""
difference of n between self,
analogous to s-s.shift(n)
Parameters
----------
arr : ndarray
n : int
number of periods
axis : int
axis to shift on
Returns
-------
shifted
"""
n = int(n)
na = np.nan
dtype = arr.dtype
is_timedelta = False
if needs_i8_conversion(arr):
dtype = np.float64
arr = arr.view('i8')
na = iNaT
is_timedelta = True
elif is_bool_dtype(dtype):
dtype = np.object_
elif is_integer_dtype(dtype):
dtype = np.float64
dtype = np.dtype(dtype)
out_arr = np.empty(arr.shape, dtype=dtype)
na_indexer = [slice(None)] * arr.ndim
na_indexer[axis] = slice(None, n) if n >= 0 else slice(n, None)
out_arr[tuple(na_indexer)] = na
if arr.ndim == 2 and arr.dtype.name in _diff_special:
f = _diff_special[arr.dtype.name]
f(arr, out_arr, n, axis)
else:
res_indexer = [slice(None)] * arr.ndim
res_indexer[axis] = slice(n, None) if n >= 0 else slice(None, n)
res_indexer = tuple(res_indexer)
lag_indexer = [slice(None)] * arr.ndim
lag_indexer[axis] = slice(None, -n) if n > 0 else slice(-n, None)
lag_indexer = tuple(lag_indexer)
# need to make sure that we account for na for datelike/timedelta
# we don't actually want to subtract these i8 numbers
if is_timedelta:
res = arr[res_indexer]
lag = arr[lag_indexer]
mask = (arr[res_indexer] == na) | (arr[lag_indexer] == na)
if mask.any():
res = res.copy()
res[mask] = 0
lag = lag.copy()
lag[mask] = 0
result = res - lag
result[mask] = na
out_arr[res_indexer] = result
else:
out_arr[res_indexer] = arr[res_indexer] - arr[lag_indexer]
if is_timedelta:
from pandas import TimedeltaIndex
out_arr = TimedeltaIndex(out_arr.ravel().astype('int64')).asi8.reshape(
out_arr.shape).astype('timedelta64[ns]')
return out_arr