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internals.pyx
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from collections import defaultdict
import weakref
cimport cython
from cpython.slice cimport PySlice_GetIndicesEx
from cython cimport Py_ssize_t
cdef extern from "Python.h":
# TODO(cython3): from cpython.pyport cimport PY_SSIZE_T_MAX
Py_ssize_t PY_SSIZE_T_MAX
import numpy as np
cimport numpy as cnp
from numpy cimport (
NPY_INTP,
int64_t,
intp_t,
ndarray,
)
cnp.import_array()
from pandas._libs.algos import ensure_int64
from pandas._libs.arrays cimport NDArrayBacked
from pandas._libs.util cimport (
is_array,
is_integer_object,
)
@cython.final
@cython.freelist(32)
cdef class BlockPlacement:
cdef:
slice _as_slice
ndarray _as_array # Note: this still allows `None`; will be intp_t
bint _has_slice, _has_array, _is_known_slice_like
def __cinit__(self, val):
cdef:
slice slc
self._as_slice = None
self._as_array = None
self._has_slice = False
self._has_array = False
if is_integer_object(val):
slc = slice(val, val + 1, 1)
self._as_slice = slc
self._has_slice = True
elif isinstance(val, slice):
slc = slice_canonize(val)
if slc.start != slc.stop:
self._as_slice = slc
self._has_slice = True
else:
arr = np.empty(0, dtype=np.intp)
self._as_array = arr
self._has_array = True
else:
# Cython memoryview interface requires ndarray to be writeable.
if (
not is_array(val)
or not cnp.PyArray_ISWRITEABLE(val)
or (<ndarray>val).descr.type_num != cnp.NPY_INTP
):
arr = np.require(val, dtype=np.intp, requirements="W")
else:
arr = val
# Caller is responsible for ensuring arr.ndim == 1
self._as_array = arr
self._has_array = True
def __str__(self) -> str:
cdef:
slice s = self._ensure_has_slice()
if s is not None:
v = self._as_slice
else:
v = self._as_array
return f"{type(self).__name__}({v})"
def __repr__(self) -> str:
return str(self)
def __len__(self) -> int:
cdef:
slice s = self._ensure_has_slice()
if s is not None:
return slice_len(s)
else:
return len(self._as_array)
def __iter__(self):
cdef:
slice s = self._ensure_has_slice()
Py_ssize_t start, stop, step, _
if s is not None:
start, stop, step, _ = slice_get_indices_ex(s)
return iter(range(start, stop, step))
else:
return iter(self._as_array)
@property
def as_slice(self) -> slice:
cdef:
slice s = self._ensure_has_slice()
if s is not None:
return s
else:
raise TypeError("Not slice-like")
@property
def indexer(self):
cdef:
slice s = self._ensure_has_slice()
if s is not None:
return s
else:
return self._as_array
@property
def as_array(self) -> np.ndarray:
cdef:
Py_ssize_t start, stop, _
if not self._has_array:
start, stop, step, _ = slice_get_indices_ex(self._as_slice)
# NOTE: this is the C-optimized equivalent of
# `np.arange(start, stop, step, dtype=np.intp)`
self._as_array = cnp.PyArray_Arange(start, stop, step, NPY_INTP)
self._has_array = True
return self._as_array
@property
def is_slice_like(self) -> bool:
cdef:
slice s = self._ensure_has_slice()
return s is not None
def __getitem__(self, loc):
cdef:
slice s = self._ensure_has_slice()
if s is not None:
val = slice_getitem(s, loc)
else:
val = self._as_array[loc]
if not isinstance(val, slice) and val.ndim == 0:
return val
return BlockPlacement(val)
def delete(self, loc) -> BlockPlacement:
return BlockPlacement(np.delete(self.as_array, loc, axis=0))
def append(self, others) -> BlockPlacement:
if not len(others):
return self
return BlockPlacement(
np.concatenate([self.as_array] + [o.as_array for o in others])
)
cdef BlockPlacement iadd(self, other):
cdef:
slice s = self._ensure_has_slice()
Py_ssize_t other_int, start, stop, step
if is_integer_object(other) and s is not None:
other_int = <Py_ssize_t>other
if other_int == 0:
# BlockPlacement is treated as immutable
return self
start, stop, step, _ = slice_get_indices_ex(s)
start += other_int
stop += other_int
if (step > 0 and start < 0) or (step < 0 and stop < step):
raise ValueError("iadd causes length change")
if stop < 0:
val = slice(start, None, step)
else:
val = slice(start, stop, step)
return BlockPlacement(val)
else:
newarr = self.as_array + other
if (newarr < 0).any():
raise ValueError("iadd causes length change")
val = newarr
return BlockPlacement(val)
def add(self, other) -> BlockPlacement:
# We can get here with int or ndarray
return self.iadd(other)
cdef slice _ensure_has_slice(self):
if not self._has_slice:
self._as_slice = indexer_as_slice(self._as_array)
self._has_slice = True
return self._as_slice
cpdef BlockPlacement increment_above(self, Py_ssize_t loc):
"""
Increment any entries of 'loc' or above by one.
"""
cdef:
slice nv, s = self._ensure_has_slice()
Py_ssize_t start, stop, step
ndarray[intp_t, ndim=1] newarr
if s is not None:
# see if we are either all-above or all-below, each of which
# have fastpaths available.
start, stop, step, _ = slice_get_indices_ex(s)
if start < loc and stop <= loc:
# We are entirely below, nothing to increment
return self
if start >= loc and stop >= loc:
# We are entirely above, we can efficiently increment out slice
nv = slice(start + 1, stop + 1, step)
return BlockPlacement(nv)
if loc == 0:
# fastpath where we know everything is >= 0
newarr = self.as_array + 1
return BlockPlacement(newarr)
newarr = self.as_array.copy()
newarr[newarr >= loc] += 1
return BlockPlacement(newarr)
def tile_for_unstack(self, factor: int) -> np.ndarray:
"""
Find the new mgr_locs for the un-stacked version of a Block.
"""
cdef:
slice slc = self._ensure_has_slice()
ndarray[intp_t, ndim=1] new_placement
if slc is not None and slc.step == 1:
new_slc = slice(slc.start * factor, slc.stop * factor, 1)
# equiv: np.arange(new_slc.start, new_slc.stop, dtype=np.intp)
new_placement = cnp.PyArray_Arange(new_slc.start, new_slc.stop, 1, NPY_INTP)
else:
# Note: test_pivot_table_empty_aggfunc gets here with `slc is not None`
mapped = [
# equiv: np.arange(x * factor, (x + 1) * factor, dtype=np.intp)
cnp.PyArray_Arange(x * factor, (x + 1) * factor, 1, NPY_INTP)
for x in self
]
new_placement = np.concatenate(mapped)
return new_placement
cdef slice slice_canonize(slice s):
"""
Convert slice to canonical bounded form.
"""
cdef:
Py_ssize_t start = 0, stop = 0, step = 1
if s.step is None:
step = 1
else:
step = <Py_ssize_t>s.step
if step == 0:
raise ValueError("slice step cannot be zero")
if step > 0:
if s.stop is None:
raise ValueError("unbounded slice")
stop = <Py_ssize_t>s.stop
if s.start is None:
start = 0
else:
start = <Py_ssize_t>s.start
if start > stop:
start = stop
elif step < 0:
if s.start is None:
raise ValueError("unbounded slice")
start = <Py_ssize_t>s.start
if s.stop is None:
stop = -1
else:
stop = <Py_ssize_t>s.stop
if stop > start:
stop = start
if start < 0 or (stop < 0 and s.stop is not None and step > 0):
raise ValueError("unbounded slice")
if stop < 0:
return slice(start, None, step)
else:
return slice(start, stop, step)
cpdef Py_ssize_t slice_len(slice slc, Py_ssize_t objlen=PY_SSIZE_T_MAX) except -1:
"""
Get length of a bounded slice.
The slice must not have any "open" bounds that would create dependency on
container size, i.e.:
- if ``s.step is None or s.step > 0``, ``s.stop`` is not ``None``
- if ``s.step < 0``, ``s.start`` is not ``None``
Otherwise, the result is unreliable.
"""
cdef:
Py_ssize_t start, stop, step, length
if slc is None:
raise TypeError("slc must be slice") # pragma: no cover
PySlice_GetIndicesEx(slc, objlen, &start, &stop, &step, &length)
return length
cdef (Py_ssize_t, Py_ssize_t, Py_ssize_t, Py_ssize_t) slice_get_indices_ex(
slice slc, Py_ssize_t objlen=PY_SSIZE_T_MAX
):
"""
Get (start, stop, step, length) tuple for a slice.
If `objlen` is not specified, slice must be bounded, otherwise the result
will be wrong.
"""
cdef:
Py_ssize_t start, stop, step, length
if slc is None:
raise TypeError("slc should be a slice") # pragma: no cover
PySlice_GetIndicesEx(slc, objlen, &start, &stop, &step, &length)
return start, stop, step, length
cdef slice_getitem(slice slc, ind):
cdef:
Py_ssize_t s_start, s_stop, s_step, s_len
Py_ssize_t ind_start, ind_stop, ind_step, ind_len
s_start, s_stop, s_step, s_len = slice_get_indices_ex(slc)
if isinstance(ind, slice):
ind_start, ind_stop, ind_step, ind_len = slice_get_indices_ex(ind, s_len)
if ind_step > 0 and ind_len == s_len:
# short-cut for no-op slice
if ind_len == s_len:
return slc
if ind_step < 0:
s_start = s_stop - s_step
ind_step = -ind_step
s_step *= ind_step
s_stop = s_start + ind_stop * s_step
s_start = s_start + ind_start * s_step
if s_step < 0 and s_stop < 0:
return slice(s_start, None, s_step)
else:
return slice(s_start, s_stop, s_step)
else:
# NOTE:
# this is the C-optimized equivalent of
# `np.arange(s_start, s_stop, s_step, dtype=np.intp)[ind]`
return cnp.PyArray_Arange(s_start, s_stop, s_step, NPY_INTP)[ind]
@cython.boundscheck(False)
@cython.wraparound(False)
cdef slice indexer_as_slice(intp_t[:] vals):
cdef:
Py_ssize_t i, n, start, stop
int64_t d
if vals is None:
raise TypeError("vals must be ndarray") # pragma: no cover
n = vals.shape[0]
if n == 0 or vals[0] < 0:
return None
if n == 1:
return slice(vals[0], vals[0] + 1, 1)
if vals[1] < 0:
return None
# n > 2
d = vals[1] - vals[0]
if d == 0:
return None
for i in range(2, n):
if vals[i] < 0 or vals[i] - vals[i - 1] != d:
return None
start = vals[0]
stop = start + n * d
if stop < 0 and d < 0:
return slice(start, None, d)
else:
return slice(start, stop, d)
@cython.boundscheck(False)
@cython.wraparound(False)
def get_blkno_indexers(
int64_t[:] blknos, bint group=True
) -> list[tuple[int, slice | np.ndarray]]:
"""
Enumerate contiguous runs of integers in ndarray.
Iterate over elements of `blknos` yielding ``(blkno, slice(start, stop))``
pairs for each contiguous run found.
If `group` is True and there is more than one run for a certain blkno,
``(blkno, array)`` with an array containing positions of all elements equal
to blkno.
Returns
-------
list[tuple[int, slice | np.ndarray]]
"""
# There's blkno in this function's name because it's used in block &
# blockno handling.
cdef:
int64_t cur_blkno
Py_ssize_t i, start, stop, n, diff
cnp.npy_intp tot_len
int64_t blkno
object group_dict = defaultdict(list)
ndarray[int64_t, ndim=1] arr
n = blknos.shape[0]
result = list()
if n == 0:
return result
start = 0
cur_blkno = blknos[start]
if group is False:
for i in range(1, n):
if blknos[i] != cur_blkno:
result.append((cur_blkno, slice(start, i)))
start = i
cur_blkno = blknos[i]
result.append((cur_blkno, slice(start, n)))
else:
for i in range(1, n):
if blknos[i] != cur_blkno:
group_dict[cur_blkno].append((start, i))
start = i
cur_blkno = blknos[i]
group_dict[cur_blkno].append((start, n))
for blkno, slices in group_dict.items():
if len(slices) == 1:
result.append((blkno, slice(slices[0][0], slices[0][1])))
else:
tot_len = sum(stop - start for start, stop in slices)
# equiv np.empty(tot_len, dtype=np.int64)
arr = cnp.PyArray_EMPTY(1, &tot_len, cnp.NPY_INT64, 0)
i = 0
for start, stop in slices:
for diff in range(start, stop):
arr[i] = diff
i += 1
result.append((blkno, arr))
return result
def get_blkno_placements(blknos, group: bool = True):
"""
Parameters
----------
blknos : np.ndarray[int64]
group : bool, default True
Returns
-------
iterator
yield (blkno, BlockPlacement)
"""
blknos = ensure_int64(blknos)
for blkno, indexer in get_blkno_indexers(blknos, group):
yield blkno, BlockPlacement(indexer)
@cython.boundscheck(False)
@cython.wraparound(False)
cpdef update_blklocs_and_blknos(
ndarray[intp_t, ndim=1] blklocs,
ndarray[intp_t, ndim=1] blknos,
Py_ssize_t loc,
intp_t nblocks,
):
"""
Update blklocs and blknos when a new column is inserted at 'loc'.
"""
cdef:
Py_ssize_t i
cnp.npy_intp length = blklocs.shape[0] + 1
ndarray[intp_t, ndim=1] new_blklocs, new_blknos
# equiv: new_blklocs = np.empty(length, dtype=np.intp)
new_blklocs = cnp.PyArray_EMPTY(1, &length, cnp.NPY_INTP, 0)
new_blknos = cnp.PyArray_EMPTY(1, &length, cnp.NPY_INTP, 0)
for i in range(loc):
new_blklocs[i] = blklocs[i]
new_blknos[i] = blknos[i]
new_blklocs[loc] = 0
new_blknos[loc] = nblocks
for i in range(loc, length - 1):
new_blklocs[i + 1] = blklocs[i]
new_blknos[i + 1] = blknos[i]
return new_blklocs, new_blknos
def _unpickle_block(values, placement, ndim):
# We have to do some gymnastics b/c "ndim" is keyword-only
from pandas.core.internals.blocks import (
maybe_coerce_values,
new_block,
)
values = maybe_coerce_values(values)
if not isinstance(placement, BlockPlacement):
placement = BlockPlacement(placement)
return new_block(values, placement, ndim=ndim)
@cython.freelist(64)
cdef class SharedBlock:
"""
Defining __init__ in a cython class significantly improves performance.
"""
cdef:
public BlockPlacement _mgr_locs
public BlockValuesRefs refs
readonly int ndim
def __cinit__(
self,
values,
placement: BlockPlacement,
ndim: int,
refs: BlockValuesRefs | None = None,
):
"""
Parameters
----------
values : np.ndarray or ExtensionArray
We assume maybe_coerce_values has already been called.
placement : BlockPlacement
ndim : int
1 for SingleBlockManager/Series, 2 for BlockManager/DataFrame
refs: BlockValuesRefs, optional
Ref tracking object or None if block does not have any refs.
"""
self._mgr_locs = placement
self.ndim = ndim
if refs is None:
# if no refs are passed, that means we are creating a Block from
# new values that it uniquely owns -> start a new BlockValuesRefs
# object that only references this block
self.refs = BlockValuesRefs(self)
else:
# if refs are passed, this is the BlockValuesRefs object that is shared
# with the parent blocks which share the values, and a reference to this
# new block is added
refs.add_reference(self)
self.refs = refs
cpdef __reduce__(self):
args = (self.values, self.mgr_locs.indexer, self.ndim)
return _unpickle_block, args
cpdef __setstate__(self, state):
from pandas.core.construction import extract_array
self.mgr_locs = BlockPlacement(state[0])
self.values = extract_array(state[1], extract_numpy=True)
if len(state) > 2:
# we stored ndim
self.ndim = state[2]
else:
# older pickle
from pandas.core.internals.api import maybe_infer_ndim
ndim = maybe_infer_ndim(self.values, self.mgr_locs)
self.ndim = ndim
cdef class NumpyBlock(SharedBlock):
cdef:
public ndarray values
def __cinit__(
self,
ndarray values,
BlockPlacement placement,
int ndim,
refs: BlockValuesRefs | None = None,
):
# set values here; the (implicit) call to SharedBlock.__cinit__ will
# set placement, ndim and refs
self.values = values
cpdef NumpyBlock getitem_block_index(self, slice slicer):
"""
Perform __getitem__-like specialized to slicing along index.
Assumes self.ndim == 2
"""
new_values = self.values[..., slicer]
return type(self)(new_values, self._mgr_locs, ndim=self.ndim, refs=self.refs)
cdef class NDArrayBackedBlock(SharedBlock):
"""
Block backed by NDArrayBackedExtensionArray
"""
cdef public:
NDArrayBacked values
def __cinit__(
self,
NDArrayBacked values,
BlockPlacement placement,
int ndim,
refs: BlockValuesRefs | None = None,
):
# set values here; the (implicit) call to SharedBlock.__cinit__ will
# set placement, ndim and refs
self.values = values
cpdef NDArrayBackedBlock getitem_block_index(self, slice slicer):
"""
Perform __getitem__-like specialized to slicing along index.
Assumes self.ndim == 2
"""
new_values = self.values[..., slicer]
return type(self)(new_values, self._mgr_locs, ndim=self.ndim, refs=self.refs)
cdef class Block(SharedBlock):
cdef:
public object values
def __cinit__(
self,
object values,
BlockPlacement placement,
int ndim,
refs: BlockValuesRefs | None = None,
):
# set values here; the (implicit) call to SharedBlock.__cinit__ will
# set placement, ndim and refs
self.values = values
@cython.freelist(64)
cdef class BlockManager:
cdef:
public tuple blocks
public list axes
public bint _known_consolidated, _is_consolidated
public ndarray _blknos, _blklocs
def __cinit__(
self,
blocks=None,
axes=None,
verify_integrity=True,
):
# None as defaults for unpickling GH#42345
if blocks is None:
# This adds 1-2 microseconds to DataFrame(np.array([]))
return
if isinstance(blocks, list):
# Backward compat for e.g. pyarrow
blocks = tuple(blocks)
self.blocks = blocks
self.axes = axes.copy() # copy to make sure we are not remotely-mutable
# Populate known_consolidate, blknos, and blklocs lazily
self._known_consolidated = False
self._is_consolidated = False
self._blknos = None
self._blklocs = None
# -------------------------------------------------------------------
# Block Placement
def _rebuild_blknos_and_blklocs(self) -> None:
"""
Update mgr._blknos / mgr._blklocs.
"""
cdef:
intp_t blkno, i, j
cnp.npy_intp length = self.shape[0]
SharedBlock blk
BlockPlacement bp
ndarray[intp_t, ndim=1] new_blknos, new_blklocs
# equiv: np.empty(length, dtype=np.intp)
new_blknos = cnp.PyArray_EMPTY(1, &length, cnp.NPY_INTP, 0)
new_blklocs = cnp.PyArray_EMPTY(1, &length, cnp.NPY_INTP, 0)
# equiv: new_blknos.fill(-1)
cnp.PyArray_FILLWBYTE(new_blknos, -1)
cnp.PyArray_FILLWBYTE(new_blklocs, -1)
for blkno, blk in enumerate(self.blocks):
bp = blk._mgr_locs
# Iterating over `bp` is a faster equivalent to
# new_blknos[bp.indexer] = blkno
# new_blklocs[bp.indexer] = np.arange(len(bp))
for i, j in enumerate(bp):
new_blknos[j] = blkno
new_blklocs[j] = i
for i in range(length):
# faster than `for blkno in new_blknos`
# https://github.com/cython/cython/issues/4393
blkno = new_blknos[i]
# If there are any -1s remaining, this indicates that our mgr_locs
# are invalid.
if blkno == -1:
raise AssertionError("Gaps in blk ref_locs")
self._blknos = new_blknos
self._blklocs = new_blklocs
# -------------------------------------------------------------------
# Pickle
cpdef __reduce__(self):
if len(self.axes) == 1:
# SingleBlockManager, __init__ expects Block, axis
args = (self.blocks[0], self.axes[0])
else:
args = (self.blocks, self.axes)
return type(self), args
cpdef __setstate__(self, state):
from pandas.core.construction import extract_array
from pandas.core.internals.blocks import (
ensure_block_shape,
maybe_coerce_values,
new_block,
)
from pandas.core.internals.managers import ensure_index
if isinstance(state, tuple) and len(state) >= 4 and "0.14.1" in state[3]:
state = state[3]["0.14.1"]
axes = [ensure_index(ax) for ax in state["axes"]]
ndim = len(axes)
for blk in state["blocks"]:
vals = blk["values"]
# older versions may hold e.g. DatetimeIndex instead of DTA
vals = extract_array(vals, extract_numpy=True)
blk["values"] = maybe_coerce_values(ensure_block_shape(vals, ndim=ndim))
if not isinstance(blk["mgr_locs"], BlockPlacement):
blk["mgr_locs"] = BlockPlacement(blk["mgr_locs"])
nbs = [
new_block(blk["values"], blk["mgr_locs"], ndim=ndim)
for blk in state["blocks"]
]
blocks = tuple(nbs)
self.blocks = blocks
self.axes = axes
else: # pragma: no cover
raise NotImplementedError("pre-0.14.1 pickles are no longer supported")
self._post_setstate()
def _post_setstate(self) -> None:
self._is_consolidated = False
self._known_consolidated = False
self._rebuild_blknos_and_blklocs()
# -------------------------------------------------------------------
# Indexing
cdef BlockManager _get_index_slice(self, slice slobj):
cdef:
SharedBlock blk, nb
BlockManager mgr
ndarray blknos, blklocs
nbs = []
for blk in self.blocks:
nb = blk.getitem_block_index(slobj)
nbs.append(nb)
new_axes = [self.axes[0], self.axes[1]._getitem_slice(slobj)]
mgr = type(self)(tuple(nbs), new_axes, verify_integrity=False)
# We can avoid having to rebuild blklocs/blknos
blklocs = self._blklocs
blknos = self._blknos
if blknos is not None:
mgr._blknos = blknos.copy()
mgr._blklocs = blklocs.copy()
return mgr
def get_slice(self, slobj: slice, axis: int = 0) -> BlockManager:
if axis == 0:
new_blocks = self._slice_take_blocks_ax0(slobj)
elif axis == 1:
return self._get_index_slice(slobj)
else:
raise IndexError("Requested axis not found in manager")
new_axes = list(self.axes)
new_axes[axis] = new_axes[axis]._getitem_slice(slobj)
return type(self)(tuple(new_blocks), new_axes, verify_integrity=False)
cdef class BlockValuesRefs:
"""Tracks all references to a given array.
Keeps track of all blocks (through weak references) that reference the same
data.
"""
cdef:
public list referenced_blocks
def __cinit__(self, blk: SharedBlock | None = None) -> None:
if blk is not None:
self.referenced_blocks = [weakref.ref(blk)]
else:
self.referenced_blocks = []
def add_reference(self, blk: SharedBlock) -> None:
"""Adds a new reference to our reference collection.
Parameters
----------
blk: SharedBlock
The block that the new references should point to.
"""
self.referenced_blocks.append(weakref.ref(blk))
def add_index_reference(self, index: object) -> None:
"""Adds a new reference to our reference collection when creating an index.
Parameters
----------
index: object
The index that the new reference should point to.
"""
self.referenced_blocks.append(weakref.ref(index))
def has_reference(self) -> bool:
"""Checks if block has foreign references.
A reference is only relevant if it is still alive. The reference to
ourselves does not count.
Returns
-------
bool
"""
self.referenced_blocks = [
ref for ref in self.referenced_blocks if ref() is not None
]
# Checking for more references than block pointing to itself
return len(self.referenced_blocks) > 1