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1039 lines
33 KiB
1039 lines
33 KiB
6 years ago
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from __future__ import absolute_import, division, print_function
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from itertools import product
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import math
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from numbers import Integral, Number
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from operator import getitem, itemgetter
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import warnings
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import numpy as np
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from toolz import memoize, merge, pluck, concat
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from .. import core
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from ..highlevelgraph import HighLevelGraph
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from ..base import tokenize, is_dask_collection
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colon = slice(None, None, None)
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def _sanitize_index_element(ind):
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"""Sanitize a one-element index."""
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if isinstance(ind, Number):
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ind2 = int(ind)
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if ind2 != ind:
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raise IndexError("Bad index. Must be integer-like: %s" % ind)
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else:
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return ind2
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elif ind is None:
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return None
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else:
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raise TypeError("Invalid index type", type(ind), ind)
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def sanitize_index(ind):
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""" Sanitize the elements for indexing along one axis
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>>> sanitize_index([2, 3, 5])
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array([2, 3, 5])
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>>> sanitize_index([True, False, True, False])
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array([0, 2])
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>>> sanitize_index(np.array([1, 2, 3]))
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array([1, 2, 3])
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>>> sanitize_index(np.array([False, True, True]))
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array([1, 2])
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>>> type(sanitize_index(np.int32(0)))
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<class 'int'>
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>>> sanitize_index(1.0)
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1
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>>> sanitize_index(0.5)
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Traceback (most recent call last):
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...
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IndexError: Bad index. Must be integer-like: 0.5
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"""
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if ind is None:
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return None
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elif isinstance(ind, slice):
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return slice(_sanitize_index_element(ind.start),
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_sanitize_index_element(ind.stop),
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_sanitize_index_element(ind.step))
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elif isinstance(ind, Number):
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return _sanitize_index_element(ind)
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elif is_dask_collection(ind):
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return ind
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index_array = np.asanyarray(ind)
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if index_array.dtype == bool:
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nonzero = np.nonzero(index_array)
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if len(nonzero) == 1:
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# If a 1-element tuple, unwrap the element
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nonzero = nonzero[0]
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return np.asanyarray(nonzero)
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elif np.issubdtype(index_array.dtype, np.integer):
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return index_array
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elif np.issubdtype(index_array.dtype, np.floating):
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int_index = index_array.astype(np.intp)
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if np.allclose(index_array, int_index):
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return int_index
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else:
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check_int = np.isclose(index_array, int_index)
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first_err = index_array.ravel(
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)[np.flatnonzero(~check_int)[0]]
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raise IndexError("Bad index. Must be integer-like: %s" %
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first_err)
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else:
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raise TypeError("Invalid index type", type(ind), ind)
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def slice_array(out_name, in_name, blockdims, index):
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"""
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Master function for array slicing
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This function makes a new dask that slices blocks along every
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dimension and aggregates (via cartesian product) each dimension's
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slices so that the resulting block slices give the same results
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as the original slice on the original structure
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Index must be a tuple. It may contain the following types
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int, slice, list (at most one list), None
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Parameters
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----------
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in_name - string
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This is the dask variable name that will be used as input
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out_name - string
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This is the dask variable output name
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blockshape - iterable of integers
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index - iterable of integers, slices, lists, or None
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Returns
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-------
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Dict where the keys are tuples of
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(out_name, dim_index[, dim_index[, ...]])
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and the values are
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(function, (in_name, dim_index, dim_index, ...),
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(slice(...), [slice()[,...]])
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Also new blockdims with shapes of each block
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((10, 10, 10, 10), (20, 20))
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Examples
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--------
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>>> dsk, blockdims = slice_array('y', 'x', [(20, 20, 20, 20, 20)],
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... (slice(10, 35),)) # doctest: +SKIP
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>>> dsk # doctest: +SKIP
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{('y', 0): (getitem, ('x', 0), (slice(10, 20),)),
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('y', 1): (getitem, ('x', 1), (slice(0, 15),))}
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>>> blockdims # doctest: +SKIP
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((10, 15),)
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See Also
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--------
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This function works by successively unwrapping cases and passing down
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through a sequence of functions.
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slice_with_newaxis - handle None/newaxis case
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slice_wrap_lists - handle fancy indexing with lists
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slice_slices_and_integers - handle everything else
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"""
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blockdims = tuple(map(tuple, blockdims))
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# x[:, :, :] - Punt and return old value
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if all(isinstance(index, slice) and index == slice(None, None, None)
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for index in index):
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suffixes = product(*[range(len(bd)) for bd in blockdims])
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dsk = dict(((out_name,) + s, (in_name,) + s)
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for s in suffixes)
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return dsk, blockdims
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# Add in missing colons at the end as needed. x[5] -> x[5, :, :]
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not_none_count = sum(i is not None for i in index)
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missing = len(blockdims) - not_none_count
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index += (slice(None, None, None),) * missing
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# Pass down to next function
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dsk_out, bd_out = slice_with_newaxes(out_name, in_name, blockdims, index)
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bd_out = tuple(map(tuple, bd_out))
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return dsk_out, bd_out
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def slice_with_newaxes(out_name, in_name, blockdims, index):
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"""
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Handle indexing with Nones
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Strips out Nones then hands off to slice_wrap_lists
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"""
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# Strip Nones from index
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index2 = tuple([ind for ind in index if ind is not None])
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where_none = [i for i, ind in enumerate(index) if ind is None]
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where_none_orig = list(where_none)
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for i, x in enumerate(where_none):
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n = sum(isinstance(ind, Integral) for ind in index[:x])
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if n:
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where_none[i] -= n
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# Pass down and do work
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dsk, blockdims2 = slice_wrap_lists(out_name, in_name, blockdims, index2)
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if where_none:
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expand = expander(where_none)
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expand_orig = expander(where_none_orig)
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# Insert ",0" into the key: ('x', 2, 3) -> ('x', 0, 2, 0, 3)
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dsk2 = {(out_name,) + expand(k[1:], 0):
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(v[:2] + (expand_orig(v[2], None),))
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for k, v in dsk.items()
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if k[0] == out_name}
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# Add back intermediate parts of the dask that weren't the output
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dsk3 = merge(dsk2, {k: v for k, v in dsk.items() if k[0] != out_name})
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# Insert (1,) into blockdims: ((2, 2), (3, 3)) -> ((2, 2), (1,), (3, 3))
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blockdims3 = expand(blockdims2, (1,))
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return dsk3, blockdims3
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else:
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return dsk, blockdims2
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def slice_wrap_lists(out_name, in_name, blockdims, index):
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"""
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Fancy indexing along blocked array dasks
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Handles index of type list. Calls slice_slices_and_integers for the rest
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See Also
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--------
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take - handle slicing with lists ("fancy" indexing)
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slice_slices_and_integers - handle slicing with slices and integers
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"""
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assert all(isinstance(i, (slice, list, Integral, np.ndarray))
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for i in index)
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if not len(blockdims) == len(index):
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raise IndexError("Too many indices for array")
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# Do we have more than one list in the index?
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where_list = [i for i, ind in enumerate(index)
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if isinstance(ind, np.ndarray) and ind.ndim > 0]
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if len(where_list) > 1:
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raise NotImplementedError("Don't yet support nd fancy indexing")
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# Is the single list an empty list? In this case just treat it as a zero
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# length slice
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if where_list and not index[where_list[0]].size:
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index = list(index)
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index[where_list.pop()] = slice(0, 0, 1)
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index = tuple(index)
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# No lists, hooray! just use slice_slices_and_integers
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if not where_list:
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return slice_slices_and_integers(out_name, in_name, blockdims, index)
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# Replace all lists with full slices [3, 1, 0] -> slice(None, None, None)
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index_without_list = tuple(slice(None, None, None)
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if isinstance(i, np.ndarray) else i
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for i in index)
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# lists and full slices. Just use take
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if all(isinstance(i, np.ndarray) or i == slice(None, None, None)
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for i in index):
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axis = where_list[0]
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blockdims2, dsk3 = take(out_name, in_name, blockdims,
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index[where_list[0]], axis=axis)
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# Mixed case. Both slices/integers and lists. slice/integer then take
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else:
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# Do first pass without lists
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tmp = 'slice-' + tokenize((out_name, in_name, blockdims, index))
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dsk, blockdims2 = slice_slices_and_integers(tmp, in_name, blockdims, index_without_list)
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# After collapsing some axes due to int indices, adjust axis parameter
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axis = where_list[0]
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axis2 = axis - sum(1 for i, ind in enumerate(index)
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if i < axis and isinstance(ind, Integral))
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# Do work
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blockdims2, dsk2 = take(out_name, tmp, blockdims2, index[axis],
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axis=axis2)
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dsk3 = merge(dsk, dsk2)
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return dsk3, blockdims2
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def slice_slices_and_integers(out_name, in_name, blockdims, index):
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"""
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Dask array indexing with slices and integers
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See Also
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--------
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_slice_1d
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"""
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shape = tuple(map(sum, blockdims))
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for dim, ind in zip(shape, index):
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if np.isnan(dim) and ind != slice(None, None, None):
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raise ValueError("Arrays chunk sizes are unknown: %s", shape)
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assert all(isinstance(ind, (slice, Integral)) for ind in index)
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assert len(index) == len(blockdims)
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# Get a list (for each dimension) of dicts{blocknum: slice()}
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block_slices = list(map(_slice_1d, shape, blockdims, index))
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sorted_block_slices = [sorted(i.items()) for i in block_slices]
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# (in_name, 1, 1, 2), (in_name, 1, 1, 4), (in_name, 2, 1, 2), ...
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in_names = list(product([in_name], *[pluck(0, s) for s in sorted_block_slices]))
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# (out_name, 0, 0, 0), (out_name, 0, 0, 1), (out_name, 0, 1, 0), ...
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out_names = list(product([out_name],
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*[range(len(d))[::-1] if i.step and i.step < 0 else range(len(d))
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for d, i in zip(block_slices, index)
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if not isinstance(i, Integral)]))
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all_slices = list(product(*[pluck(1, s) for s in sorted_block_slices]))
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dsk_out = {out_name: (getitem, in_name, slices)
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for out_name, in_name, slices
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in zip(out_names, in_names, all_slices)}
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new_blockdims = [new_blockdim(d, db, i)
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for d, i, db in zip(shape, index, blockdims)
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if not isinstance(i, Integral)]
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return dsk_out, new_blockdims
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def _slice_1d(dim_shape, lengths, index):
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"""Returns a dict of {blocknum: slice}
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This function figures out where each slice should start in each
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block for a single dimension. If the slice won't return any elements
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in the block, that block will not be in the output.
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Parameters
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----------
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dim_shape - the number of elements in this dimension.
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This should be a positive, non-zero integer
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blocksize - the number of elements per block in this dimension
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This should be a positive, non-zero integer
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index - a description of the elements in this dimension that we want
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This might be an integer, a slice(), or an Ellipsis
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Returns
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-------
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||
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dictionary where the keys are the integer index of the blocks that
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should be sliced and the values are the slices
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Examples
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||
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--------
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Trivial slicing
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>>> _slice_1d(100, [60, 40], slice(None, None, None))
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{0: slice(None, None, None), 1: slice(None, None, None)}
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100 length array cut into length 20 pieces, slice 0:35
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>>> _slice_1d(100, [20, 20, 20, 20, 20], slice(0, 35))
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{0: slice(None, None, None), 1: slice(0, 15, 1)}
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Support irregular blocks and various slices
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>>> _slice_1d(100, [20, 10, 10, 10, 25, 25], slice(10, 35))
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{0: slice(10, 20, 1), 1: slice(None, None, None), 2: slice(0, 5, 1)}
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Support step sizes
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>>> _slice_1d(100, [15, 14, 13], slice(10, 41, 3))
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{0: slice(10, 15, 3), 1: slice(1, 14, 3), 2: slice(2, 12, 3)}
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|
|
>>> _slice_1d(100, [20, 20, 20, 20, 20], slice(0, 100, 40)) # step > blocksize
|
||
|
|
{0: slice(0, 20, 40), 2: slice(0, 20, 40), 4: slice(0, 20, 40)}
|
||
|
|
|
||
|
|
Also support indexing single elements
|
||
|
|
|
||
|
|
>>> _slice_1d(100, [20, 20, 20, 20, 20], 25)
|
||
|
|
{1: 5}
|
||
|
|
|
||
|
|
And negative slicing
|
||
|
|
|
||
|
|
>>> _slice_1d(100, [20, 20, 20, 20, 20], slice(100, 0, -3)) # doctest: +NORMALIZE_WHITESPACE
|
||
|
|
{4: slice(-1, -21, -3),
|
||
|
|
3: slice(-2, -21, -3),
|
||
|
|
2: slice(-3, -21, -3),
|
||
|
|
1: slice(-1, -21, -3),
|
||
|
|
0: slice(-2, -20, -3)}
|
||
|
|
|
||
|
|
>>> _slice_1d(100, [20, 20, 20, 20, 20], slice(100, 12, -3)) # doctest: +NORMALIZE_WHITESPACE
|
||
|
|
{4: slice(-1, -21, -3),
|
||
|
|
3: slice(-2, -21, -3),
|
||
|
|
2: slice(-3, -21, -3),
|
||
|
|
1: slice(-1, -21, -3),
|
||
|
|
0: slice(-2, -8, -3)}
|
||
|
|
|
||
|
|
>>> _slice_1d(100, [20, 20, 20, 20, 20], slice(100, -12, -3))
|
||
|
|
{4: slice(-1, -12, -3)}
|
||
|
|
"""
|
||
|
|
chunk_boundaries = np.cumsum(lengths, dtype=np.int64)
|
||
|
|
|
||
|
|
if isinstance(index, Integral):
|
||
|
|
# use right-side search to be consistent with previous result
|
||
|
|
i = chunk_boundaries.searchsorted(index, side='right')
|
||
|
|
if i > 0:
|
||
|
|
# the very first chunk has no relative shift
|
||
|
|
ind = index - chunk_boundaries[i - 1]
|
||
|
|
else:
|
||
|
|
ind = index
|
||
|
|
return {int(i): int(ind)}
|
||
|
|
|
||
|
|
assert isinstance(index, slice)
|
||
|
|
|
||
|
|
if index == colon:
|
||
|
|
return {k: colon for k in range(len(lengths))}
|
||
|
|
|
||
|
|
step = index.step or 1
|
||
|
|
if step > 0:
|
||
|
|
start = index.start or 0
|
||
|
|
stop = index.stop if index.stop is not None else dim_shape
|
||
|
|
else:
|
||
|
|
start = index.start if index.start is not None else dim_shape - 1
|
||
|
|
start = dim_shape - 1 if start >= dim_shape else start
|
||
|
|
stop = -(dim_shape + 1) if index.stop is None else index.stop
|
||
|
|
|
||
|
|
# posify start and stop
|
||
|
|
if start < 0:
|
||
|
|
start += dim_shape
|
||
|
|
if stop < 0:
|
||
|
|
stop += dim_shape
|
||
|
|
|
||
|
|
d = dict()
|
||
|
|
if step > 0:
|
||
|
|
istart = chunk_boundaries.searchsorted(start, side='right')
|
||
|
|
istop = chunk_boundaries.searchsorted(stop, side='left')
|
||
|
|
|
||
|
|
# the bound is not exactly tight; make it tighter?
|
||
|
|
istop = min(istop + 1, len(lengths))
|
||
|
|
|
||
|
|
# jump directly to istart
|
||
|
|
if istart > 0:
|
||
|
|
start = start - chunk_boundaries[istart - 1]
|
||
|
|
stop = stop - chunk_boundaries[istart - 1]
|
||
|
|
|
||
|
|
for i in range(istart, istop):
|
||
|
|
length = lengths[i]
|
||
|
|
if start < length and stop > 0:
|
||
|
|
d[i] = slice(start, min(stop, length), step)
|
||
|
|
start = (start - length) % step
|
||
|
|
else:
|
||
|
|
start = start - length
|
||
|
|
stop -= length
|
||
|
|
else:
|
||
|
|
rstart = start # running start
|
||
|
|
|
||
|
|
istart = chunk_boundaries.searchsorted(start, side='left')
|
||
|
|
istop = chunk_boundaries.searchsorted(stop, side='right')
|
||
|
|
|
||
|
|
# the bound is not exactly tight; make it tighter?
|
||
|
|
istart = min(istart + 1, len(chunk_boundaries) - 1)
|
||
|
|
istop = max(istop - 1, -1)
|
||
|
|
|
||
|
|
for i in range(istart, istop, -1):
|
||
|
|
chunk_stop = chunk_boundaries[i]
|
||
|
|
# create a chunk start and stop
|
||
|
|
if i == 0:
|
||
|
|
chunk_start = 0
|
||
|
|
else:
|
||
|
|
chunk_start = chunk_boundaries[i - 1]
|
||
|
|
|
||
|
|
# if our slice is in this chunk
|
||
|
|
if (chunk_start <= rstart < chunk_stop) and (rstart > stop):
|
||
|
|
d[i] = slice(rstart - chunk_stop,
|
||
|
|
max(chunk_start - chunk_stop - 1,
|
||
|
|
stop - chunk_stop),
|
||
|
|
step)
|
||
|
|
|
||
|
|
# compute the next running start point,
|
||
|
|
offset = (rstart - (chunk_start - 1)) % step
|
||
|
|
rstart = chunk_start + offset - 1
|
||
|
|
|
||
|
|
# replace 0:20:1 with : if appropriate
|
||
|
|
for k, v in d.items():
|
||
|
|
if v == slice(0, lengths[k], 1):
|
||
|
|
d[k] = slice(None, None, None)
|
||
|
|
|
||
|
|
if not d: # special case x[:0]
|
||
|
|
d[0] = slice(0, 0, 1)
|
||
|
|
|
||
|
|
return d
|
||
|
|
|
||
|
|
|
||
|
|
def partition_by_size(sizes, seq):
|
||
|
|
"""
|
||
|
|
|
||
|
|
>>> partition_by_size([10, 20, 10], [1, 5, 9, 12, 29, 35])
|
||
|
|
[array([1, 5, 9]), array([ 2, 19]), array([5])]
|
||
|
|
"""
|
||
|
|
seq = np.asanyarray(seq)
|
||
|
|
left = np.empty(len(sizes) + 1, dtype=int)
|
||
|
|
left[0] = 0
|
||
|
|
|
||
|
|
right = np.cumsum(sizes, out=left[1:])
|
||
|
|
locations = np.empty(len(sizes) + 1, dtype=int)
|
||
|
|
locations[0] = 0
|
||
|
|
locations[1:] = np.searchsorted(seq, right)
|
||
|
|
return [(seq[j:k] - l)
|
||
|
|
for j, k, l in zip(locations[:-1], locations[1:], left)]
|
||
|
|
|
||
|
|
|
||
|
|
def issorted(seq):
|
||
|
|
""" Is sequence sorted?
|
||
|
|
|
||
|
|
>>> issorted([1, 2, 3])
|
||
|
|
True
|
||
|
|
>>> issorted([3, 1, 2])
|
||
|
|
False
|
||
|
|
"""
|
||
|
|
if len(seq) == 0:
|
||
|
|
return True
|
||
|
|
return np.all(seq[:-1] <= seq[1:])
|
||
|
|
|
||
|
|
|
||
|
|
def slicing_plan(chunks, index):
|
||
|
|
""" Construct a plan to slice chunks with the given index
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
chunks : Tuple[int]
|
||
|
|
One dimensions worth of chunking information
|
||
|
|
index : np.ndarray[int]
|
||
|
|
The index passed to slice on that dimension
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
out : List[Tuple[int, np.ndarray]]
|
||
|
|
A list of chunk/sub-index pairs corresponding to each output chunk
|
||
|
|
"""
|
||
|
|
index = np.asanyarray(index)
|
||
|
|
cum_chunks = np.cumsum(chunks)
|
||
|
|
|
||
|
|
chunk_locations = np.searchsorted(cum_chunks, index, side='right')
|
||
|
|
where = np.where(np.diff(chunk_locations))[0] + 1
|
||
|
|
where = np.concatenate([[0], where, [len(chunk_locations)]])
|
||
|
|
|
||
|
|
out = []
|
||
|
|
for i in range(len(where) - 1):
|
||
|
|
sub_index = index[where[i]:where[i + 1]]
|
||
|
|
chunk = chunk_locations[where[i]]
|
||
|
|
if chunk > 0:
|
||
|
|
sub_index = sub_index - cum_chunks[chunk - 1]
|
||
|
|
out.append((chunk, sub_index))
|
||
|
|
|
||
|
|
return out
|
||
|
|
|
||
|
|
|
||
|
|
def take(outname, inname, chunks, index, axis=0):
|
||
|
|
""" Index array with an iterable of index
|
||
|
|
|
||
|
|
Handles a single index by a single list
|
||
|
|
|
||
|
|
Mimics ``np.take``
|
||
|
|
|
||
|
|
>>> chunks, dsk = take('y', 'x', [(20, 20, 20, 20)], [5, 1, 47, 3], axis=0)
|
||
|
|
>>> chunks
|
||
|
|
((2, 1, 1),)
|
||
|
|
>>> dsk # doctest: +SKIP
|
||
|
|
{('y', 0): (getitem, (np.concatenate, [(getitem, ('x', 0), ([1, 3, 5],)),
|
||
|
|
(getitem, ('x', 2), ([7],))],
|
||
|
|
0),
|
||
|
|
(2, 0, 4, 1))}
|
||
|
|
|
||
|
|
When list is sorted we retain original block structure
|
||
|
|
|
||
|
|
>>> chunks, dsk = take('y', 'x', [(20, 20, 20, 20)], [1, 3, 5, 47], axis=0)
|
||
|
|
>>> chunks
|
||
|
|
((3, 1),)
|
||
|
|
>>> dsk # doctest: +SKIP
|
||
|
|
{('y', 0): (getitem, ('x', 0), ([1, 3, 5],)),
|
||
|
|
('y', 2): (getitem, ('x', 2), ([7],))}
|
||
|
|
"""
|
||
|
|
plan = slicing_plan(chunks[axis], index)
|
||
|
|
if len(plan) >= len(chunks[axis]) * 10:
|
||
|
|
factor = math.ceil(len(plan) / len(chunks[axis]))
|
||
|
|
from .core import PerformanceWarning
|
||
|
|
warnings.warn("Slicing with an out-of-order index is generating %d "
|
||
|
|
"times more chunks" % factor, PerformanceWarning,
|
||
|
|
stacklevel=6)
|
||
|
|
|
||
|
|
index_lists = [idx for _, idx in plan]
|
||
|
|
where_index = [i for i, _ in plan]
|
||
|
|
|
||
|
|
dims = [range(len(bd)) for bd in chunks]
|
||
|
|
|
||
|
|
indims = list(dims)
|
||
|
|
indims[axis] = list(range(len(where_index)))
|
||
|
|
keys = list(product([outname], *indims))
|
||
|
|
|
||
|
|
outdims = list(dims)
|
||
|
|
outdims[axis] = where_index
|
||
|
|
slices = [[colon] * len(bd) for bd in chunks]
|
||
|
|
slices[axis] = index_lists
|
||
|
|
slices = list(product(*slices))
|
||
|
|
inkeys = list(product([inname], *outdims))
|
||
|
|
values = [(getitem, inkey, slc) for inkey, slc in zip(inkeys, slices)]
|
||
|
|
|
||
|
|
chunks2 = list(chunks)
|
||
|
|
chunks2[axis] = tuple(map(len, index_lists))
|
||
|
|
dsk = dict(zip(keys, values))
|
||
|
|
return tuple(chunks2), dsk
|
||
|
|
|
||
|
|
|
||
|
|
def posify_index(shape, ind):
|
||
|
|
""" Flip negative indices around to positive ones
|
||
|
|
|
||
|
|
>>> posify_index(10, 3)
|
||
|
|
3
|
||
|
|
>>> posify_index(10, -3)
|
||
|
|
7
|
||
|
|
>>> posify_index(10, [3, -3])
|
||
|
|
array([3, 7])
|
||
|
|
|
||
|
|
>>> posify_index((10, 20), (3, -3))
|
||
|
|
(3, 17)
|
||
|
|
>>> posify_index((10, 20), (3, [3, 4, -3])) # doctest: +NORMALIZE_WHITESPACE
|
||
|
|
(3, array([ 3, 4, 17]))
|
||
|
|
"""
|
||
|
|
if isinstance(ind, tuple):
|
||
|
|
return tuple(map(posify_index, shape, ind))
|
||
|
|
if isinstance(ind, Integral):
|
||
|
|
if ind < 0 and not math.isnan(shape):
|
||
|
|
return ind + shape
|
||
|
|
else:
|
||
|
|
return ind
|
||
|
|
if isinstance(ind, (np.ndarray, list)) and not math.isnan(shape):
|
||
|
|
ind = np.asanyarray(ind)
|
||
|
|
return np.where(ind < 0, ind + shape, ind)
|
||
|
|
return ind
|
||
|
|
|
||
|
|
|
||
|
|
@memoize
|
||
|
|
def _expander(where):
|
||
|
|
if not where:
|
||
|
|
def expand(seq, val):
|
||
|
|
return seq
|
||
|
|
return expand
|
||
|
|
else:
|
||
|
|
decl = """def expand(seq, val):
|
||
|
|
return ({left}) + tuple({right})
|
||
|
|
"""
|
||
|
|
left = []
|
||
|
|
j = 0
|
||
|
|
for i in range(max(where) + 1):
|
||
|
|
if i in where:
|
||
|
|
left.append("val, ")
|
||
|
|
else:
|
||
|
|
left.append("seq[%d], " % j)
|
||
|
|
j += 1
|
||
|
|
right = "seq[%d:]" % j
|
||
|
|
left = "".join(left)
|
||
|
|
decl = decl.format(**locals())
|
||
|
|
ns = {}
|
||
|
|
exec(compile(decl, "<dynamic>", "exec"), ns, ns)
|
||
|
|
return ns['expand']
|
||
|
|
|
||
|
|
|
||
|
|
def expander(where):
|
||
|
|
"""Create a function to insert value at many locations in sequence.
|
||
|
|
|
||
|
|
>>> expander([0, 2])(['a', 'b', 'c'], 'z')
|
||
|
|
('z', 'a', 'z', 'b', 'c')
|
||
|
|
"""
|
||
|
|
return _expander(tuple(where))
|
||
|
|
|
||
|
|
|
||
|
|
def new_blockdim(dim_shape, lengths, index):
|
||
|
|
"""
|
||
|
|
|
||
|
|
>>> new_blockdim(100, [20, 10, 20, 10, 40], slice(0, 90, 2))
|
||
|
|
[10, 5, 10, 5, 15]
|
||
|
|
|
||
|
|
>>> new_blockdim(100, [20, 10, 20, 10, 40], [5, 1, 30, 22])
|
||
|
|
[4]
|
||
|
|
|
||
|
|
>>> new_blockdim(100, [20, 10, 20, 10, 40], slice(90, 10, -2))
|
||
|
|
[16, 5, 10, 5, 4]
|
||
|
|
"""
|
||
|
|
if index == slice(None, None, None):
|
||
|
|
return lengths
|
||
|
|
if isinstance(index, list):
|
||
|
|
return [len(index)]
|
||
|
|
assert not isinstance(index, Integral)
|
||
|
|
pairs = sorted(_slice_1d(dim_shape, lengths, index).items(),
|
||
|
|
key=itemgetter(0))
|
||
|
|
slices = [slice(0, lengths[i], 1) if slc == slice(None, None, None) else slc
|
||
|
|
for i, slc in pairs]
|
||
|
|
if isinstance(index, slice) and index.step and index.step < 0:
|
||
|
|
slices = slices[::-1]
|
||
|
|
return [int(math.ceil((1. * slc.stop - slc.start) / slc.step)) for slc in slices]
|
||
|
|
|
||
|
|
|
||
|
|
def replace_ellipsis(n, index):
|
||
|
|
""" Replace ... with slices, :, : ,:
|
||
|
|
|
||
|
|
>>> replace_ellipsis(4, (3, Ellipsis, 2))
|
||
|
|
(3, slice(None, None, None), slice(None, None, None), 2)
|
||
|
|
|
||
|
|
>>> replace_ellipsis(2, (Ellipsis, None))
|
||
|
|
(slice(None, None, None), slice(None, None, None), None)
|
||
|
|
"""
|
||
|
|
# Careful about using in or index because index may contain arrays
|
||
|
|
isellipsis = [i for i, ind in enumerate(index) if ind is Ellipsis]
|
||
|
|
if not isellipsis:
|
||
|
|
return index
|
||
|
|
else:
|
||
|
|
loc = isellipsis[0]
|
||
|
|
extra_dimensions = n - (len(index) - sum(i is None for i in index) - 1)
|
||
|
|
return (index[:loc] + (slice(None, None, None),) * extra_dimensions +
|
||
|
|
index[loc + 1:])
|
||
|
|
|
||
|
|
|
||
|
|
def normalize_slice(idx, dim):
|
||
|
|
""" Normalize slices to canonical form
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
idx: slice or other index
|
||
|
|
dim: dimension length
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> normalize_slice(slice(0, 10, 1), 10)
|
||
|
|
slice(None, None, None)
|
||
|
|
"""
|
||
|
|
|
||
|
|
if isinstance(idx, slice):
|
||
|
|
if math.isnan(dim):
|
||
|
|
return idx
|
||
|
|
start, stop, step = idx.indices(dim)
|
||
|
|
if step > 0:
|
||
|
|
if start == 0:
|
||
|
|
start = None
|
||
|
|
if stop >= dim:
|
||
|
|
stop = None
|
||
|
|
if step == 1:
|
||
|
|
step = None
|
||
|
|
if stop is not None and start is not None and stop < start:
|
||
|
|
stop = start
|
||
|
|
elif step < 0:
|
||
|
|
if start >= dim - 1:
|
||
|
|
start = None
|
||
|
|
if stop < 0:
|
||
|
|
stop = None
|
||
|
|
return slice(start, stop, step)
|
||
|
|
return idx
|
||
|
|
|
||
|
|
|
||
|
|
def normalize_index(idx, shape):
|
||
|
|
""" Normalize slicing indexes
|
||
|
|
|
||
|
|
1. Replaces ellipses with many full slices
|
||
|
|
2. Adds full slices to end of index
|
||
|
|
3. Checks bounding conditions
|
||
|
|
4. Replaces numpy arrays with lists
|
||
|
|
5. Posify's integers and lists
|
||
|
|
6. Normalizes slices to canonical form
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> normalize_index(1, (10,))
|
||
|
|
(1,)
|
||
|
|
>>> normalize_index(-1, (10,))
|
||
|
|
(9,)
|
||
|
|
>>> normalize_index([-1], (10,))
|
||
|
|
(array([9]),)
|
||
|
|
>>> normalize_index(slice(-3, 10, 1), (10,))
|
||
|
|
(slice(7, None, None),)
|
||
|
|
>>> normalize_index((Ellipsis, None), (10,))
|
||
|
|
(slice(None, None, None), None)
|
||
|
|
"""
|
||
|
|
if not isinstance(idx, tuple):
|
||
|
|
idx = (idx,)
|
||
|
|
idx = replace_ellipsis(len(shape), idx)
|
||
|
|
n_sliced_dims = 0
|
||
|
|
for i in idx:
|
||
|
|
if hasattr(i, 'ndim') and i.ndim >= 1:
|
||
|
|
n_sliced_dims += i.ndim
|
||
|
|
elif i is None:
|
||
|
|
continue
|
||
|
|
else:
|
||
|
|
n_sliced_dims += 1
|
||
|
|
idx = idx + (slice(None),) * (len(shape) - n_sliced_dims)
|
||
|
|
if len([i for i in idx if i is not None]) > len(shape):
|
||
|
|
raise IndexError("Too many indices for array")
|
||
|
|
|
||
|
|
none_shape = []
|
||
|
|
i = 0
|
||
|
|
for ind in idx:
|
||
|
|
if ind is not None:
|
||
|
|
none_shape.append(shape[i])
|
||
|
|
i += 1
|
||
|
|
else:
|
||
|
|
none_shape.append(None)
|
||
|
|
|
||
|
|
for i, d in zip(idx, none_shape):
|
||
|
|
if d is not None:
|
||
|
|
check_index(i, d)
|
||
|
|
idx = tuple(map(sanitize_index, idx))
|
||
|
|
idx = tuple(map(normalize_slice, idx, none_shape))
|
||
|
|
idx = posify_index(none_shape, idx)
|
||
|
|
return idx
|
||
|
|
|
||
|
|
|
||
|
|
def check_index(ind, dimension):
|
||
|
|
""" Check validity of index for a given dimension
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> check_index(3, 5)
|
||
|
|
>>> check_index(5, 5)
|
||
|
|
Traceback (most recent call last):
|
||
|
|
...
|
||
|
|
IndexError: Index is not smaller than dimension 5 >= 5
|
||
|
|
|
||
|
|
>>> check_index(6, 5)
|
||
|
|
Traceback (most recent call last):
|
||
|
|
...
|
||
|
|
IndexError: Index is not smaller than dimension 6 >= 5
|
||
|
|
|
||
|
|
>>> check_index(-1, 5)
|
||
|
|
>>> check_index(-6, 5)
|
||
|
|
Traceback (most recent call last):
|
||
|
|
...
|
||
|
|
IndexError: Negative index is not greater than negative dimension -6 <= -5
|
||
|
|
|
||
|
|
>>> check_index([1, 2], 5)
|
||
|
|
>>> check_index([6, 3], 5)
|
||
|
|
Traceback (most recent call last):
|
||
|
|
...
|
||
|
|
IndexError: Index out of bounds 5
|
||
|
|
|
||
|
|
>>> check_index(slice(0, 3), 5)
|
||
|
|
|
||
|
|
>>> check_index([True], 1)
|
||
|
|
>>> check_index([True, True], 3)
|
||
|
|
Traceback (most recent call last):
|
||
|
|
...
|
||
|
|
IndexError: Boolean array length 2 doesn't equal dimension 3
|
||
|
|
>>> check_index([True, True, True], 1)
|
||
|
|
Traceback (most recent call last):
|
||
|
|
...
|
||
|
|
IndexError: Boolean array length 3 doesn't equal dimension 1
|
||
|
|
"""
|
||
|
|
# unknown dimension, assumed to be in bounds
|
||
|
|
if np.isnan(dimension):
|
||
|
|
return
|
||
|
|
elif isinstance(ind, (list, np.ndarray)):
|
||
|
|
x = np.asanyarray(ind)
|
||
|
|
if x.dtype == bool:
|
||
|
|
if x.size != dimension:
|
||
|
|
raise IndexError(
|
||
|
|
"Boolean array length %s doesn't equal dimension %s" %
|
||
|
|
(x.size, dimension))
|
||
|
|
elif (x >= dimension).any() or (x < -dimension).any():
|
||
|
|
raise IndexError("Index out of bounds %s" % dimension)
|
||
|
|
elif isinstance(ind, slice):
|
||
|
|
return
|
||
|
|
elif is_dask_collection(ind):
|
||
|
|
return
|
||
|
|
elif ind is None:
|
||
|
|
return
|
||
|
|
|
||
|
|
elif ind >= dimension:
|
||
|
|
raise IndexError("Index is not smaller than dimension %d >= %d" %
|
||
|
|
(ind, dimension))
|
||
|
|
|
||
|
|
elif ind < -dimension:
|
||
|
|
msg = "Negative index is not greater than negative dimension %d <= -%d"
|
||
|
|
raise IndexError(msg % (ind, dimension))
|
||
|
|
|
||
|
|
|
||
|
|
def slice_with_int_dask_array(x, index):
|
||
|
|
""" Slice x with at most one 1D dask arrays of ints.
|
||
|
|
|
||
|
|
This is a helper function of :meth:`Array.__getitem__`.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
x: Array
|
||
|
|
index: tuple with as many elements as x.ndim, among which there are
|
||
|
|
one or more Array's with dtype=int
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
tuple of (sliced x, new index)
|
||
|
|
|
||
|
|
where the new index is the same as the input, but with slice(None)
|
||
|
|
replaced to the original slicer where a 1D filter has been applied and
|
||
|
|
one less element where a zero-dimensional filter has been applied.
|
||
|
|
"""
|
||
|
|
from .core import Array
|
||
|
|
|
||
|
|
assert len(index) == x.ndim
|
||
|
|
fancy_indexes = [
|
||
|
|
isinstance(idx, (tuple, list)) or
|
||
|
|
(isinstance(idx, (np.ndarray, Array)) and idx.ndim > 0)
|
||
|
|
for idx in index
|
||
|
|
]
|
||
|
|
if sum(fancy_indexes) > 1:
|
||
|
|
raise NotImplementedError("Don't yet support nd fancy indexing)")
|
||
|
|
|
||
|
|
out_index = []
|
||
|
|
dropped_axis_cnt = 0
|
||
|
|
for in_axis, idx in enumerate(index):
|
||
|
|
out_axis = in_axis - dropped_axis_cnt
|
||
|
|
if isinstance(idx, Array) and idx.dtype.kind in 'iu':
|
||
|
|
if idx.ndim == 0:
|
||
|
|
idx = idx[np.newaxis]
|
||
|
|
x = slice_with_int_dask_array_on_axis(x, idx, out_axis)
|
||
|
|
x = x[tuple(
|
||
|
|
0 if i == out_axis else slice(None)
|
||
|
|
for i in range(x.ndim)
|
||
|
|
)]
|
||
|
|
dropped_axis_cnt += 1
|
||
|
|
elif idx.ndim == 1:
|
||
|
|
x = slice_with_int_dask_array_on_axis(x, idx, out_axis)
|
||
|
|
out_index.append(slice(None))
|
||
|
|
else:
|
||
|
|
raise NotImplementedError(
|
||
|
|
"Slicing with dask.array of ints only permitted when "
|
||
|
|
"the indexer has zero or one dimensions")
|
||
|
|
else:
|
||
|
|
out_index.append(idx)
|
||
|
|
return x, tuple(out_index)
|
||
|
|
|
||
|
|
|
||
|
|
def slice_with_int_dask_array_on_axis(x, idx, axis):
|
||
|
|
""" Slice a ND dask array with a 1D dask arrays of ints along the given
|
||
|
|
axis.
|
||
|
|
|
||
|
|
This is a helper function of :func:`slice_with_int_dask_array`.
|
||
|
|
"""
|
||
|
|
from .core import Array, blockwise, from_array
|
||
|
|
from . import chunk
|
||
|
|
|
||
|
|
assert 0 <= axis < x.ndim
|
||
|
|
|
||
|
|
if np.isnan(x.chunks[axis]).any():
|
||
|
|
raise NotImplementedError("Slicing an array with unknown chunks with "
|
||
|
|
"a dask.array of ints is not supported")
|
||
|
|
|
||
|
|
# Calculate the offset at which each chunk starts along axis
|
||
|
|
# e.g. chunks=(..., (5, 3, 4), ...) -> offset=[0, 5, 8]
|
||
|
|
offset = np.roll(np.cumsum(x.chunks[axis]), 1)
|
||
|
|
offset[0] = 0
|
||
|
|
offset = from_array(offset, chunks=1)
|
||
|
|
# Tamper with the declared chunks of offset to make blockwise align it with
|
||
|
|
# x[axis]
|
||
|
|
offset = Array(offset.dask, offset.name, (x.chunks[axis], ), offset.dtype)
|
||
|
|
|
||
|
|
# Define axis labels for blockwise
|
||
|
|
x_axes = tuple(range(x.ndim))
|
||
|
|
idx_axes = (x.ndim, ) # arbitrary index not already in x_axes
|
||
|
|
offset_axes = (axis, )
|
||
|
|
p_axes = x_axes[:axis + 1] + idx_axes + x_axes[axis + 1:]
|
||
|
|
y_axes = x_axes[:axis] + idx_axes + x_axes[axis + 1:]
|
||
|
|
|
||
|
|
# Calculate the cartesian product of every chunk of x vs every chunk of idx
|
||
|
|
p = blockwise(chunk.slice_with_int_dask_array,
|
||
|
|
p_axes, x, x_axes, idx, idx_axes, offset, offset_axes,
|
||
|
|
x_size=x.shape[axis], axis=axis, dtype=x.dtype)
|
||
|
|
|
||
|
|
# Aggregate on the chunks of x along axis
|
||
|
|
y = blockwise(chunk.slice_with_int_dask_array_aggregate,
|
||
|
|
y_axes, idx, idx_axes, p, p_axes,
|
||
|
|
concatenate=True, x_chunks=x.chunks[axis], axis=axis,
|
||
|
|
dtype=x.dtype)
|
||
|
|
return y
|
||
|
|
|
||
|
|
|
||
|
|
def slice_with_bool_dask_array(x, index):
|
||
|
|
""" Slice x with one or more dask arrays of bools
|
||
|
|
|
||
|
|
This is a helper function of `Array.__getitem__`.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
x: Array
|
||
|
|
index: tuple with as many elements as x.ndim, among which there are
|
||
|
|
one or more Array's with dtype=bool
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
tuple of (sliced x, new index)
|
||
|
|
|
||
|
|
where the new index is the same as the input, but with slice(None)
|
||
|
|
replaced to the original slicer when a filter has been applied.
|
||
|
|
|
||
|
|
Note: The sliced x will have nan chunks on the sliced axes.
|
||
|
|
"""
|
||
|
|
from .core import Array, blockwise, elemwise
|
||
|
|
|
||
|
|
out_index = [slice(None)
|
||
|
|
if isinstance(ind, Array) and ind.dtype == bool
|
||
|
|
else ind
|
||
|
|
for ind in index]
|
||
|
|
|
||
|
|
if len(index) == 1 and index[0].ndim == x.ndim:
|
||
|
|
y = elemwise(getitem, x, *index, dtype=x.dtype)
|
||
|
|
name = 'getitem-' + tokenize(x, index)
|
||
|
|
dsk = {(name, i): k for i, k in enumerate(core.flatten(y.__dask_keys__()))}
|
||
|
|
chunks = ((np.nan,) * y.npartitions,)
|
||
|
|
graph = HighLevelGraph.from_collections(name, dsk, dependencies=[y])
|
||
|
|
return Array(graph, name, chunks, x.dtype), out_index
|
||
|
|
|
||
|
|
if any(isinstance(ind, Array) and ind.dtype == bool and ind.ndim != 1
|
||
|
|
for ind in index):
|
||
|
|
raise NotImplementedError("Slicing with dask.array of bools only permitted when "
|
||
|
|
"the indexer has only one dimension or when "
|
||
|
|
"it has the same dimension as the sliced "
|
||
|
|
"array")
|
||
|
|
indexes = [ind
|
||
|
|
if isinstance(ind, Array) and ind.dtype == bool
|
||
|
|
else slice(None)
|
||
|
|
for ind in index]
|
||
|
|
|
||
|
|
arginds = []
|
||
|
|
i = 0
|
||
|
|
for ind in indexes:
|
||
|
|
if isinstance(ind, Array) and ind.dtype == bool:
|
||
|
|
new = (ind, tuple(range(i, i + ind.ndim)))
|
||
|
|
i += x.ndim
|
||
|
|
else:
|
||
|
|
new = (slice(None), None)
|
||
|
|
i += 1
|
||
|
|
arginds.append(new)
|
||
|
|
|
||
|
|
arginds = list(concat(arginds))
|
||
|
|
|
||
|
|
out = blockwise(getitem_variadic, tuple(range(x.ndim)), x, tuple(range(x.ndim)),
|
||
|
|
*arginds, dtype=x.dtype)
|
||
|
|
|
||
|
|
chunks = []
|
||
|
|
for ind, chunk in zip(index, out.chunks):
|
||
|
|
if isinstance(ind, Array) and ind.dtype == bool:
|
||
|
|
chunks.append((np.nan,) * len(chunk))
|
||
|
|
else:
|
||
|
|
chunks.append(chunk)
|
||
|
|
out._chunks = tuple(chunks)
|
||
|
|
return out, tuple(out_index)
|
||
|
|
|
||
|
|
|
||
|
|
def getitem_variadic(x, *index):
|
||
|
|
return x[index]
|