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824 lines
23 KiB
824 lines
23 KiB
from collections import defaultdict
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import cython
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from cython import Py_ssize_t
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from cpython.slice cimport PySlice_GetIndicesEx
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cdef extern from "Python.h":
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Py_ssize_t PY_SSIZE_T_MAX
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import numpy as np
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cimport numpy as cnp
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from numpy cimport (
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NPY_INTP,
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int64_t,
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intp_t,
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ndarray,
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)
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cnp.import_array()
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from pandas._libs.algos import ensure_int64
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from pandas._libs.arrays cimport NDArrayBacked
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from pandas._libs.util cimport (
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is_array,
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is_integer_object,
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)
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@cython.final
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@cython.freelist(32)
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cdef class BlockPlacement:
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# __slots__ = '_as_slice', '_as_array', '_len'
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cdef:
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slice _as_slice
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ndarray _as_array # Note: this still allows `None`; will be intp_t
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bint _has_slice, _has_array, _is_known_slice_like
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def __cinit__(self, val):
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cdef:
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slice slc
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self._as_slice = None
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self._as_array = None
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self._has_slice = False
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self._has_array = False
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if is_integer_object(val):
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slc = slice(val, val + 1, 1)
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self._as_slice = slc
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self._has_slice = True
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elif isinstance(val, slice):
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slc = slice_canonize(val)
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if slc.start != slc.stop:
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self._as_slice = slc
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self._has_slice = True
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else:
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arr = np.empty(0, dtype=np.intp)
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self._as_array = arr
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self._has_array = True
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else:
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# Cython memoryview interface requires ndarray to be writeable.
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if (
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not is_array(val)
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or not cnp.PyArray_ISWRITEABLE(val)
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or (<ndarray>val).descr.type_num != cnp.NPY_INTP
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):
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arr = np.require(val, dtype=np.intp, requirements='W')
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else:
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arr = val
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# Caller is responsible for ensuring arr.ndim == 1
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self._as_array = arr
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self._has_array = True
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def __str__(self) -> str:
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cdef:
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slice s = self._ensure_has_slice()
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if s is not None:
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v = self._as_slice
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else:
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v = self._as_array
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return f"{type(self).__name__}({v})"
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def __repr__(self) -> str:
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return str(self)
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def __len__(self) -> int:
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cdef:
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slice s = self._ensure_has_slice()
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if s is not None:
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return slice_len(s)
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else:
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return len(self._as_array)
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def __iter__(self):
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cdef:
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slice s = self._ensure_has_slice()
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Py_ssize_t start, stop, step, _
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if s is not None:
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start, stop, step, _ = slice_get_indices_ex(s)
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return iter(range(start, stop, step))
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else:
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return iter(self._as_array)
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@property
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def as_slice(self) -> slice:
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cdef:
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slice s = self._ensure_has_slice()
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if s is not None:
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return s
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else:
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raise TypeError("Not slice-like")
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@property
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def indexer(self):
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cdef:
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slice s = self._ensure_has_slice()
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if s is not None:
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return s
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else:
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return self._as_array
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@property
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def as_array(self) -> np.ndarray:
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cdef:
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Py_ssize_t start, stop, end, _
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if not self._has_array:
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start, stop, step, _ = slice_get_indices_ex(self._as_slice)
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# NOTE: this is the C-optimized equivalent of
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# `np.arange(start, stop, step, dtype=np.intp)`
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self._as_array = cnp.PyArray_Arange(start, stop, step, NPY_INTP)
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self._has_array = True
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return self._as_array
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@property
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def is_slice_like(self) -> bool:
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cdef:
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slice s = self._ensure_has_slice()
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return s is not None
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def __getitem__(self, loc):
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cdef:
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slice s = self._ensure_has_slice()
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if s is not None:
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val = slice_getitem(s, loc)
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else:
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val = self._as_array[loc]
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if not isinstance(val, slice) and val.ndim == 0:
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return val
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return BlockPlacement(val)
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def delete(self, loc) -> BlockPlacement:
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return BlockPlacement(np.delete(self.as_array, loc, axis=0))
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def append(self, others) -> BlockPlacement:
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if not len(others):
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return self
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return BlockPlacement(
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np.concatenate([self.as_array] + [o.as_array for o in others])
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)
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cdef BlockPlacement iadd(self, other):
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cdef:
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slice s = self._ensure_has_slice()
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Py_ssize_t other_int, start, stop, step
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if is_integer_object(other) and s is not None:
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other_int = <Py_ssize_t>other
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if other_int == 0:
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# BlockPlacement is treated as immutable
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return self
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start, stop, step, _ = slice_get_indices_ex(s)
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start += other_int
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stop += other_int
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if (step > 0 and start < 0) or (step < 0 and stop < step):
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raise ValueError("iadd causes length change")
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if stop < 0:
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val = slice(start, None, step)
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else:
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val = slice(start, stop, step)
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return BlockPlacement(val)
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else:
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newarr = self.as_array + other
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if (newarr < 0).any():
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raise ValueError("iadd causes length change")
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val = newarr
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return BlockPlacement(val)
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def add(self, other) -> BlockPlacement:
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# We can get here with int or ndarray
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return self.iadd(other)
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cdef slice _ensure_has_slice(self):
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if not self._has_slice:
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self._as_slice = indexer_as_slice(self._as_array)
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self._has_slice = True
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return self._as_slice
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cpdef BlockPlacement increment_above(self, Py_ssize_t loc):
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"""
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Increment any entries of 'loc' or above by one.
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"""
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cdef:
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slice nv, s = self._ensure_has_slice()
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Py_ssize_t other_int, start, stop, step
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ndarray[intp_t, ndim=1] newarr
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if s is not None:
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# see if we are either all-above or all-below, each of which
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# have fastpaths available.
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start, stop, step, _ = slice_get_indices_ex(s)
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if start < loc and stop <= loc:
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# We are entirely below, nothing to increment
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return self
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if start >= loc and stop >= loc:
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# We are entirely above, we can efficiently increment out slice
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nv = slice(start + 1, stop + 1, step)
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return BlockPlacement(nv)
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if loc == 0:
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# fastpath where we know everything is >= 0
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newarr = self.as_array + 1
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return BlockPlacement(newarr)
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newarr = self.as_array.copy()
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newarr[newarr >= loc] += 1
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return BlockPlacement(newarr)
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def tile_for_unstack(self, factor: int) -> np.ndarray:
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"""
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Find the new mgr_locs for the un-stacked version of a Block.
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"""
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cdef:
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slice slc = self._ensure_has_slice()
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slice new_slice
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ndarray[intp_t, ndim=1] new_placement
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if slc is not None and slc.step == 1:
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new_slc = slice(slc.start * factor, slc.stop * factor, 1)
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# equiv: np.arange(new_slc.start, new_slc.stop, dtype=np.intp)
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new_placement = cnp.PyArray_Arange(new_slc.start, new_slc.stop, 1, NPY_INTP)
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else:
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# Note: test_pivot_table_empty_aggfunc gets here with `slc is not None`
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mapped = [
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# equiv: np.arange(x * factor, (x + 1) * factor, dtype=np.intp)
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cnp.PyArray_Arange(x * factor, (x + 1) * factor, 1, NPY_INTP)
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for x in self
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]
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new_placement = np.concatenate(mapped)
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return new_placement
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cdef slice slice_canonize(slice s):
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"""
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Convert slice to canonical bounded form.
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"""
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cdef:
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Py_ssize_t start = 0, stop = 0, step = 1
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if s.step is None:
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step = 1
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else:
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step = <Py_ssize_t>s.step
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if step == 0:
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raise ValueError("slice step cannot be zero")
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if step > 0:
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if s.stop is None:
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raise ValueError("unbounded slice")
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stop = <Py_ssize_t>s.stop
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if s.start is None:
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start = 0
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else:
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start = <Py_ssize_t>s.start
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if start > stop:
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start = stop
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elif step < 0:
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if s.start is None:
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raise ValueError("unbounded slice")
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start = <Py_ssize_t>s.start
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if s.stop is None:
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stop = -1
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else:
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stop = <Py_ssize_t>s.stop
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if stop > start:
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stop = start
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if start < 0 or (stop < 0 and s.stop is not None and step > 0):
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raise ValueError("unbounded slice")
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if stop < 0:
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return slice(start, None, step)
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else:
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return slice(start, stop, step)
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cpdef Py_ssize_t slice_len(slice slc, Py_ssize_t objlen=PY_SSIZE_T_MAX) except -1:
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"""
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Get length of a bounded slice.
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The slice must not have any "open" bounds that would create dependency on
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container size, i.e.:
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- if ``s.step is None or s.step > 0``, ``s.stop`` is not ``None``
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- if ``s.step < 0``, ``s.start`` is not ``None``
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Otherwise, the result is unreliable.
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"""
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cdef:
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Py_ssize_t start, stop, step, length
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if slc is None:
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raise TypeError("slc must be slice") # pragma: no cover
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PySlice_GetIndicesEx(slc, objlen, &start, &stop, &step, &length)
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return length
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cdef (Py_ssize_t, Py_ssize_t, Py_ssize_t, Py_ssize_t) slice_get_indices_ex(
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slice slc, Py_ssize_t objlen=PY_SSIZE_T_MAX
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):
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"""
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Get (start, stop, step, length) tuple for a slice.
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If `objlen` is not specified, slice must be bounded, otherwise the result
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will be wrong.
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"""
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cdef:
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Py_ssize_t start, stop, step, length
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if slc is None:
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raise TypeError("slc should be a slice") # pragma: no cover
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PySlice_GetIndicesEx(slc, objlen, &start, &stop, &step, &length)
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return start, stop, step, length
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cdef slice_getitem(slice slc, ind):
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cdef:
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Py_ssize_t s_start, s_stop, s_step, s_len
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Py_ssize_t ind_start, ind_stop, ind_step, ind_len
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s_start, s_stop, s_step, s_len = slice_get_indices_ex(slc)
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if isinstance(ind, slice):
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ind_start, ind_stop, ind_step, ind_len = slice_get_indices_ex(ind, s_len)
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if ind_step > 0 and ind_len == s_len:
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# short-cut for no-op slice
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if ind_len == s_len:
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return slc
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if ind_step < 0:
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s_start = s_stop - s_step
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ind_step = -ind_step
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s_step *= ind_step
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s_stop = s_start + ind_stop * s_step
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s_start = s_start + ind_start * s_step
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if s_step < 0 and s_stop < 0:
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return slice(s_start, None, s_step)
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else:
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return slice(s_start, s_stop, s_step)
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else:
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# NOTE:
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# this is the C-optimized equivalent of
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# `np.arange(s_start, s_stop, s_step, dtype=np.intp)[ind]`
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return cnp.PyArray_Arange(s_start, s_stop, s_step, NPY_INTP)[ind]
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@cython.boundscheck(False)
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@cython.wraparound(False)
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cdef slice indexer_as_slice(intp_t[:] vals):
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cdef:
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Py_ssize_t i, n, start, stop
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int64_t d
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if vals is None:
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raise TypeError("vals must be ndarray") # pragma: no cover
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n = vals.shape[0]
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if n == 0 or vals[0] < 0:
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return None
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if n == 1:
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return slice(vals[0], vals[0] + 1, 1)
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if vals[1] < 0:
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return None
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# n > 2
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d = vals[1] - vals[0]
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if d == 0:
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return None
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for i in range(2, n):
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if vals[i] < 0 or vals[i] - vals[i - 1] != d:
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return None
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start = vals[0]
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stop = start + n * d
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if stop < 0 and d < 0:
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return slice(start, None, d)
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else:
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return slice(start, stop, d)
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@cython.boundscheck(False)
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@cython.wraparound(False)
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def get_blkno_indexers(
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int64_t[:] blknos, bint group=True
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) -> list[tuple[int, slice | np.ndarray]]:
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"""
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Enumerate contiguous runs of integers in ndarray.
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Iterate over elements of `blknos` yielding ``(blkno, slice(start, stop))``
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pairs for each contiguous run found.
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If `group` is True and there is more than one run for a certain blkno,
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``(blkno, array)`` with an array containing positions of all elements equal
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to blkno.
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Returns
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-------
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list[tuple[int, slice | np.ndarray]]
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"""
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# There's blkno in this function's name because it's used in block &
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# blockno handling.
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cdef:
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int64_t cur_blkno
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Py_ssize_t i, start, stop, n, diff
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cnp.npy_intp tot_len
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int64_t blkno
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object group_dict = defaultdict(list)
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ndarray[int64_t, ndim=1] arr
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n = blknos.shape[0]
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result = list()
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start = 0
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cur_blkno = blknos[start]
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if n == 0:
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pass
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elif group is False:
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for i in range(1, n):
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if blknos[i] != cur_blkno:
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result.append((cur_blkno, slice(start, i)))
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start = i
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cur_blkno = blknos[i]
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result.append((cur_blkno, slice(start, n)))
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else:
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for i in range(1, n):
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if blknos[i] != cur_blkno:
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group_dict[cur_blkno].append((start, i))
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start = i
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cur_blkno = blknos[i]
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group_dict[cur_blkno].append((start, n))
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for blkno, slices in group_dict.items():
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if len(slices) == 1:
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result.append((blkno, slice(slices[0][0], slices[0][1])))
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else:
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tot_len = sum(stop - start for start, stop in slices)
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# equiv np.empty(tot_len, dtype=np.int64)
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arr = cnp.PyArray_EMPTY(1, &tot_len, cnp.NPY_INT64, 0)
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i = 0
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for start, stop in slices:
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for diff in range(start, stop):
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arr[i] = diff
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i += 1
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result.append((blkno, arr))
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return result
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def get_blkno_placements(blknos, group: bool = True):
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"""
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Parameters
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----------
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blknos : np.ndarray[int64]
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group : bool, default True
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Returns
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-------
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iterator
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yield (blkno, BlockPlacement)
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"""
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blknos = ensure_int64(blknos)
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for blkno, indexer in get_blkno_indexers(blknos, group):
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yield blkno, BlockPlacement(indexer)
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@cython.boundscheck(False)
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@cython.wraparound(False)
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cpdef update_blklocs_and_blknos(
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ndarray[intp_t, ndim=1] blklocs,
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ndarray[intp_t, ndim=1] blknos,
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Py_ssize_t loc,
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intp_t nblocks,
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):
|
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"""
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Update blklocs and blknos when a new column is inserted at 'loc'.
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"""
|
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cdef:
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Py_ssize_t i
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cnp.npy_intp length = len(blklocs) + 1
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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 new_block
|
|
|
|
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
|
|
readonly int ndim
|
|
|
|
def __cinit__(self, values, placement: BlockPlacement, ndim: int):
|
|
"""
|
|
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
|
|
"""
|
|
self._mgr_locs = placement
|
|
self.ndim = ndim
|
|
|
|
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):
|
|
# set values here the (implicit) call to SharedBlock.__cinit__ will
|
|
# set placement and ndim
|
|
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)
|
|
|
|
|
|
cdef class NDArrayBackedBlock(SharedBlock):
|
|
"""
|
|
Block backed by NDArrayBackedExtensionArray
|
|
"""
|
|
cdef public:
|
|
NDArrayBacked values
|
|
|
|
def __cinit__(self, NDArrayBacked values, BlockPlacement placement, int ndim):
|
|
# set values here the (implicit) call to SharedBlock.__cinit__ will
|
|
# set placement and ndim
|
|
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)
|
|
|
|
|
|
cdef class Block(SharedBlock):
|
|
cdef:
|
|
public object values
|
|
|
|
def __cinit__(self, object values, BlockPlacement placement, int ndim):
|
|
# set values here the (implicit) call to SharedBlock.__cinit__ will
|
|
# set placement and ndim
|
|
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,
|
|
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"] = ensure_block_shape(vals, ndim=ndim)
|
|
|
|
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, 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)
|
|
|