1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226
|
from __future__ import annotations
import enum
import functools
import math
import operator
from collections import Counter, defaultdict
from collections.abc import Callable, Hashable, Iterable, Mapping
from contextlib import suppress
from dataclasses import dataclass, field
from datetime import timedelta
from typing import TYPE_CHECKING, Any, cast, overload
import numpy as np
import pandas as pd
from numpy.typing import DTypeLike
from packaging.version import Version
from xarray.core import duck_array_ops
from xarray.core.coordinate_transform import CoordinateTransform
from xarray.core.nputils import NumpyVIndexAdapter
from xarray.core.types import T_Xarray
from xarray.core.utils import (
NDArrayMixin,
either_dict_or_kwargs,
get_valid_numpy_dtype,
is_allowed_extension_array,
is_allowed_extension_array_dtype,
is_duck_array,
is_duck_dask_array,
is_full_slice,
is_scalar,
is_valid_numpy_dtype,
to_0d_array,
)
from xarray.namedarray.parallelcompat import get_chunked_array_type
from xarray.namedarray.pycompat import array_type, integer_types, is_chunked_array
if TYPE_CHECKING:
from xarray.core.extension_array import PandasExtensionArray
from xarray.core.indexes import Index
from xarray.core.types import Self
from xarray.core.variable import Variable
from xarray.namedarray._typing import _Shape, duckarray
from xarray.namedarray.parallelcompat import ChunkManagerEntrypoint
BasicIndexerType = int | np.integer | slice
OuterIndexerType = BasicIndexerType | np.ndarray[Any, np.dtype[np.integer]]
@dataclass
class IndexSelResult:
"""Index query results.
Attributes
----------
dim_indexers: dict
A dictionary where keys are array dimensions and values are
location-based indexers.
indexes: dict, optional
New indexes to replace in the resulting DataArray or Dataset.
variables : dict, optional
New variables to replace in the resulting DataArray or Dataset.
drop_coords : list, optional
Coordinate(s) to drop in the resulting DataArray or Dataset.
drop_indexes : list, optional
Index(es) to drop in the resulting DataArray or Dataset.
rename_dims : dict, optional
A dictionary in the form ``{old_dim: new_dim}`` for dimension(s) to
rename in the resulting DataArray or Dataset.
"""
dim_indexers: dict[Any, Any]
indexes: dict[Any, Index] = field(default_factory=dict)
variables: dict[Any, Variable] = field(default_factory=dict)
drop_coords: list[Hashable] = field(default_factory=list)
drop_indexes: list[Hashable] = field(default_factory=list)
rename_dims: dict[Any, Hashable] = field(default_factory=dict)
def as_tuple(self):
"""Unlike ``dataclasses.astuple``, return a shallow copy.
See https://stackoverflow.com/a/51802661
"""
return (
self.dim_indexers,
self.indexes,
self.variables,
self.drop_coords,
self.drop_indexes,
self.rename_dims,
)
def merge_sel_results(results: list[IndexSelResult]) -> IndexSelResult:
all_dims_count = Counter([dim for res in results for dim in res.dim_indexers])
duplicate_dims = {k: v for k, v in all_dims_count.items() if v > 1}
if duplicate_dims:
# TODO: this message is not right when combining indexe(s) queries with
# location-based indexing on a dimension with no dimension-coordinate (failback)
fmt_dims = [
f"{dim!r}: {count} indexes involved"
for dim, count in duplicate_dims.items()
]
raise ValueError(
"Xarray does not support label-based selection with more than one index "
"over the following dimension(s):\n"
+ "\n".join(fmt_dims)
+ "\nSuggestion: use a multi-index for each of those dimension(s)."
)
dim_indexers = {}
indexes = {}
variables = {}
drop_coords = []
drop_indexes = []
rename_dims = {}
for res in results:
dim_indexers.update(res.dim_indexers)
indexes.update(res.indexes)
variables.update(res.variables)
drop_coords += res.drop_coords
drop_indexes += res.drop_indexes
rename_dims.update(res.rename_dims)
return IndexSelResult(
dim_indexers, indexes, variables, drop_coords, drop_indexes, rename_dims
)
def group_indexers_by_index(
obj: T_Xarray,
indexers: Mapping[Any, Any],
options: Mapping[str, Any],
) -> list[tuple[Index, dict[Any, Any]]]:
"""Returns a list of unique indexes and their corresponding indexers."""
unique_indexes = {}
grouped_indexers: Mapping[int | None, dict] = defaultdict(dict)
for key, label in indexers.items():
index: Index = obj.xindexes.get(key, None)
if index is not None:
index_id = id(index)
unique_indexes[index_id] = index
grouped_indexers[index_id][key] = label
elif key in obj.coords:
raise KeyError(f"no index found for coordinate {key!r}")
elif key not in obj.dims:
raise KeyError(
f"{key!r} is not a valid dimension or coordinate for "
f"{obj.__class__.__name__} with dimensions {obj.dims!r}"
)
elif len(options):
raise ValueError(
f"cannot supply selection options {options!r} for dimension {key!r}"
"that has no associated coordinate or index"
)
else:
# key is a dimension without a "dimension-coordinate"
# failback to location-based selection
# TODO: depreciate this implicit behavior and suggest using isel instead?
unique_indexes[None] = None
grouped_indexers[None][key] = label
return [(unique_indexes[k], grouped_indexers[k]) for k in unique_indexes]
def map_index_queries(
obj: T_Xarray,
indexers: Mapping[Any, Any],
method=None,
tolerance: int | float | Iterable[int | float] | None = None,
**indexers_kwargs: Any,
) -> IndexSelResult:
"""Execute index queries from a DataArray / Dataset and label-based indexers
and return the (merged) query results.
"""
from xarray.core.dataarray import DataArray
# TODO benbovy - flexible indexes: remove when custom index options are available
if method is None and tolerance is None:
options = {}
else:
options = {"method": method, "tolerance": tolerance}
indexers = either_dict_or_kwargs(indexers, indexers_kwargs, "map_index_queries")
grouped_indexers = group_indexers_by_index(obj, indexers, options)
results = []
for index, labels in grouped_indexers:
if index is None:
# forward dimension indexers with no index/coordinate
results.append(IndexSelResult(labels))
else:
results.append(index.sel(labels, **options))
merged = merge_sel_results(results)
# drop dimension coordinates found in dimension indexers
# (also drop multi-index if any)
# (.sel() already ensures alignment)
for k, v in merged.dim_indexers.items():
if isinstance(v, DataArray):
if k in v._indexes:
v = v.reset_index(k)
drop_coords = [name for name in v._coords if name in merged.dim_indexers]
merged.dim_indexers[k] = v.drop_vars(drop_coords)
return merged
def expanded_indexer(key, ndim):
"""Given a key for indexing an ndarray, return an equivalent key which is a
tuple with length equal to the number of dimensions.
The expansion is done by replacing all `Ellipsis` items with the right
number of full slices and then padding the key with full slices so that it
reaches the appropriate dimensionality.
"""
if not isinstance(key, tuple):
# numpy treats non-tuple keys equivalent to tuples of length 1
key = (key,)
new_key = []
# handling Ellipsis right is a little tricky, see:
# https://numpy.org/doc/stable/reference/arrays.indexing.html#advanced-indexing
found_ellipsis = False
for k in key:
if k is Ellipsis:
if not found_ellipsis:
new_key.extend((ndim + 1 - len(key)) * [slice(None)])
found_ellipsis = True
else:
new_key.append(slice(None))
else:
new_key.append(k)
if len(new_key) > ndim:
raise IndexError("too many indices")
new_key.extend((ndim - len(new_key)) * [slice(None)])
return tuple(new_key)
def normalize_slice(sl: slice, size: int) -> slice:
"""
Ensure that given slice only contains positive start and stop values
(stop can be -1 for full-size slices with negative steps, e.g. [-10::-1])
Examples
--------
>>> normalize_slice(slice(0, 9), 10)
slice(0, 9, 1)
>>> normalize_slice(slice(0, -1), 10)
slice(0, 9, 1)
"""
return slice(*sl.indices(size))
def _expand_slice(slice_: slice, size: int) -> np.ndarray[Any, np.dtype[np.integer]]:
"""
Expand slice to an array containing only positive integers.
Examples
--------
>>> _expand_slice(slice(0, 9), 10)
array([0, 1, 2, 3, 4, 5, 6, 7, 8])
>>> _expand_slice(slice(0, -1), 10)
array([0, 1, 2, 3, 4, 5, 6, 7, 8])
"""
sl = normalize_slice(slice_, size)
return np.arange(sl.start, sl.stop, sl.step)
def slice_slice(old_slice: slice, applied_slice: slice, size: int) -> slice:
"""Given a slice and the size of the dimension to which it will be applied,
index it with another slice to return a new slice equivalent to applying
the slices sequentially
"""
old_slice = normalize_slice(old_slice, size)
size_after_old_slice = len(range(old_slice.start, old_slice.stop, old_slice.step))
if size_after_old_slice == 0:
# nothing left after applying first slice
return slice(0)
applied_slice = normalize_slice(applied_slice, size_after_old_slice)
start = old_slice.start + applied_slice.start * old_slice.step
if start < 0:
# nothing left after applying second slice
# (can only happen for old_slice.step < 0, e.g. [10::-1], [20:])
return slice(0)
stop = old_slice.start + applied_slice.stop * old_slice.step
if stop < 0:
stop = None
step = old_slice.step * applied_slice.step
return slice(start, stop, step)
def normalize_array(
array: np.ndarray[Any, np.dtype[np.integer]], size: int
) -> np.ndarray[Any, np.dtype[np.integer]]:
"""
Ensure that the given array only contains positive values.
Examples
--------
>>> normalize_array(np.array([-1, -2, -3, -4]), 10)
array([9, 8, 7, 6])
>>> normalize_array(np.array([-5, 3, 5, -1, 8]), 12)
array([ 7, 3, 5, 11, 8])
"""
if np.issubdtype(array.dtype, np.unsignedinteger):
return array
return np.where(array >= 0, array, array + size)
def slice_slice_by_array(
old_slice: slice,
array: np.ndarray[Any, np.dtype[np.integer]],
size: int,
) -> np.ndarray[Any, np.dtype[np.integer]]:
"""Given a slice and the size of the dimension to which it will be applied,
index it with an array to return a new array equivalent to applying
the slices sequentially
Examples
--------
>>> slice_slice_by_array(slice(2, 10), np.array([1, 3, 5]), 12)
array([3, 5, 7])
>>> slice_slice_by_array(slice(1, None, 2), np.array([1, 3, 7, 8]), 20)
array([ 3, 7, 15, 17])
>>> slice_slice_by_array(slice(None, None, -1), np.array([2, 4, 7]), 20)
array([17, 15, 12])
"""
# to get a concrete slice, limited to the size of the array
normalized_slice = normalize_slice(old_slice, size)
size_after_slice = len(range(*normalized_slice.indices(size)))
normalized_array = normalize_array(array, size_after_slice)
new_indexer = normalized_array * normalized_slice.step + normalized_slice.start
if np.any(new_indexer >= size):
raise IndexError("indices out of bounds") # TODO: more helpful error message
return new_indexer
def _index_indexer_1d(
old_indexer: OuterIndexerType,
applied_indexer: OuterIndexerType,
size: int,
) -> OuterIndexerType:
if is_full_slice(applied_indexer):
# shortcut for the usual case
return old_indexer
if is_full_slice(old_indexer):
# shortcut for full slices
return applied_indexer
indexer: OuterIndexerType
if isinstance(old_indexer, slice):
if isinstance(applied_indexer, slice):
indexer = slice_slice(old_indexer, applied_indexer, size)
elif isinstance(applied_indexer, integer_types):
indexer = range(*old_indexer.indices(size))[applied_indexer]
else:
indexer = slice_slice_by_array(old_indexer, applied_indexer, size)
elif isinstance(old_indexer, np.ndarray):
indexer = old_indexer[applied_indexer]
else:
# should be unreachable
raise ValueError("cannot index integers. Please open an issuec-")
return indexer
class ExplicitIndexer:
"""Base class for explicit indexer objects.
ExplicitIndexer objects wrap a tuple of values given by their ``tuple``
property. These tuples should always have length equal to the number of
dimensions on the indexed array.
Do not instantiate BaseIndexer objects directly: instead, use one of the
sub-classes BasicIndexer, OuterIndexer or VectorizedIndexer.
"""
__slots__ = ("_key",)
def __init__(self, key: tuple[Any, ...]):
if type(self) is ExplicitIndexer:
raise TypeError("cannot instantiate base ExplicitIndexer objects")
self._key = tuple(key)
@property
def tuple(self) -> tuple[Any, ...]:
return self._key
def __repr__(self) -> str:
return f"{type(self).__name__}({self.tuple})"
@overload
def as_integer_or_none(value: int) -> int: ...
@overload
def as_integer_or_none(value: None) -> None: ...
def as_integer_or_none(value: int | None) -> int | None:
return None if value is None else operator.index(value)
def as_integer_slice(value: slice) -> slice:
start = as_integer_or_none(value.start)
stop = as_integer_or_none(value.stop)
step = as_integer_or_none(value.step)
return slice(start, stop, step)
class IndexCallable:
"""Provide getitem and setitem syntax for callable objects."""
__slots__ = ("getter", "setter")
def __init__(
self, getter: Callable[..., Any], setter: Callable[..., Any] | None = None
):
self.getter = getter
self.setter = setter
def __getitem__(self, key: Any) -> Any:
return self.getter(key)
def __setitem__(self, key: Any, value: Any) -> None:
if self.setter is None:
raise NotImplementedError(
"Setting values is not supported for this indexer."
)
self.setter(key, value)
class BasicIndexer(ExplicitIndexer):
"""Tuple for basic indexing.
All elements should be int or slice objects. Indexing follows NumPy's
rules for basic indexing: each axis is independently sliced and axes
indexed with an integer are dropped from the result.
"""
__slots__ = ()
def __init__(self, key: tuple[BasicIndexerType, ...]):
if not isinstance(key, tuple):
raise TypeError(f"key must be a tuple: {key!r}")
new_key = []
for k in key:
if isinstance(k, integer_types):
k = int(k)
elif isinstance(k, slice):
k = as_integer_slice(k)
else:
raise TypeError(
f"unexpected indexer type for {type(self).__name__}: {k!r}"
)
new_key.append(k)
super().__init__(tuple(new_key))
class OuterIndexer(ExplicitIndexer):
"""Tuple for outer/orthogonal indexing.
All elements should be int, slice or 1-dimensional np.ndarray objects with
an integer dtype. Indexing is applied independently along each axis, and
axes indexed with an integer are dropped from the result. This type of
indexing works like MATLAB/Fortran.
"""
__slots__ = ()
def __init__(
self,
key: tuple[BasicIndexerType | np.ndarray[Any, np.dtype[np.generic]], ...],
):
if not isinstance(key, tuple):
raise TypeError(f"key must be a tuple: {key!r}")
new_key = []
for k in key:
if isinstance(k, integer_types):
k = int(k)
elif isinstance(k, slice):
k = as_integer_slice(k)
elif is_duck_array(k):
if not np.issubdtype(k.dtype, np.integer):
raise TypeError(
f"invalid indexer array, does not have integer dtype: {k!r}"
)
if k.ndim > 1: # type: ignore[union-attr]
raise TypeError(
f"invalid indexer array for {type(self).__name__}; must be scalar "
f"or have 1 dimension: {k!r}"
)
k = duck_array_ops.astype(k, np.int64, copy=False)
else:
raise TypeError(
f"unexpected indexer type for {type(self).__name__}: {k!r}"
)
new_key.append(k)
super().__init__(tuple(new_key))
class VectorizedIndexer(ExplicitIndexer):
"""Tuple for vectorized indexing.
All elements should be slice or N-dimensional np.ndarray objects with an
integer dtype and the same number of dimensions. Indexing follows proposed
rules for np.ndarray.vindex, which matches NumPy's advanced indexing rules
(including broadcasting) except sliced axes are always moved to the end:
https://github.com/numpy/numpy/pull/6256
"""
__slots__ = ()
def __init__(self, key: tuple[slice | np.ndarray[Any, np.dtype[np.generic]], ...]):
if not isinstance(key, tuple):
raise TypeError(f"key must be a tuple: {key!r}")
new_key = []
ndim = None
for k in key:
if isinstance(k, slice):
k = as_integer_slice(k)
elif is_duck_array(k):
if not np.issubdtype(k.dtype, np.integer):
raise TypeError(
f"invalid indexer array, does not have integer dtype: {k!r}"
)
if ndim is None:
ndim = k.ndim # type: ignore[union-attr]
elif ndim != k.ndim: # type: ignore[union-attr]
ndims = [k.ndim for k in key if isinstance(k, np.ndarray)]
raise ValueError(
"invalid indexer key: ndarray arguments "
f"have different numbers of dimensions: {ndims}"
)
k = duck_array_ops.astype(k, np.int64, copy=False)
else:
raise TypeError(
f"unexpected indexer type for {type(self).__name__}: {k!r}"
)
new_key.append(k)
super().__init__(tuple(new_key))
class ExplicitlyIndexed:
"""Mixin to mark support for Indexer subclasses in indexing."""
__slots__ = ()
def __array__(
self, dtype: np.typing.DTypeLike = None, /, *, copy: bool | None = None
) -> np.ndarray:
# Leave casting to an array up to the underlying array type.
if Version(np.__version__) >= Version("2.0.0"):
return np.asarray(self.get_duck_array(), dtype=dtype, copy=copy)
else:
return np.asarray(self.get_duck_array(), dtype=dtype)
def get_duck_array(self):
return self.array
class ExplicitlyIndexedNDArrayMixin(NDArrayMixin, ExplicitlyIndexed):
__slots__ = ()
def get_duck_array(self):
raise NotImplementedError
async def async_get_duck_array(self):
raise NotImplementedError
def _oindex_get(self, indexer: OuterIndexer):
raise NotImplementedError(
f"{self.__class__.__name__}._oindex_get method should be overridden"
)
def _vindex_get(self, indexer: VectorizedIndexer):
raise NotImplementedError(
f"{self.__class__.__name__}._vindex_get method should be overridden"
)
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
raise NotImplementedError(
f"{self.__class__.__name__}._oindex_set method should be overridden"
)
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
raise NotImplementedError(
f"{self.__class__.__name__}._vindex_set method should be overridden"
)
def _check_and_raise_if_non_basic_indexer(self, indexer: ExplicitIndexer) -> None:
if isinstance(indexer, VectorizedIndexer | OuterIndexer):
raise TypeError(
"Vectorized indexing with vectorized or outer indexers is not supported. "
"Please use .vindex and .oindex properties to index the array."
)
@property
def oindex(self) -> IndexCallable:
return IndexCallable(self._oindex_get, self._oindex_set)
@property
def vindex(self) -> IndexCallable:
return IndexCallable(self._vindex_get, self._vindex_set)
class IndexingAdapter(ExplicitlyIndexedNDArrayMixin):
"""Marker class for indexing adapters.
These classes translate between Xarray's indexing semantics and the underlying array's
indexing semantics.
"""
def get_duck_array(self):
key = BasicIndexer((slice(None),) * self.ndim)
return self[key]
async def async_get_duck_array(self):
"""These classes are applied to in-memory arrays, so specific async support isn't needed."""
return self.get_duck_array()
class ImplicitToExplicitIndexingAdapter(NDArrayMixin):
"""Wrap an array, converting tuples into the indicated explicit indexer."""
__slots__ = ("array", "indexer_cls")
def __init__(self, array, indexer_cls: type[ExplicitIndexer] = BasicIndexer):
self.array = as_indexable(array)
self.indexer_cls = indexer_cls
def __array__(
self, dtype: np.typing.DTypeLike = None, /, *, copy: bool | None = None
) -> np.ndarray:
if Version(np.__version__) >= Version("2.0.0"):
return np.asarray(self.get_duck_array(), dtype=dtype, copy=copy)
else:
return np.asarray(self.get_duck_array(), dtype=dtype)
def get_duck_array(self):
return self.array.get_duck_array()
def __getitem__(self, key: Any):
key = expanded_indexer(key, self.ndim)
indexer = self.indexer_cls(key)
result = apply_indexer(self.array, indexer)
if isinstance(result, ExplicitlyIndexed):
return type(self)(result, self.indexer_cls)
else:
# Sometimes explicitly indexed arrays return NumPy arrays or
# scalars.
return result
class LazilyIndexedArray(ExplicitlyIndexedNDArrayMixin):
"""Wrap an array to make basic and outer indexing lazy."""
__slots__ = ("_shape", "array", "key")
def __init__(self, array: Any, key: ExplicitIndexer | None = None):
"""
Parameters
----------
array : array_like
Array like object to index.
key : ExplicitIndexer, optional
Array indexer. If provided, it is assumed to already be in
canonical expanded form.
"""
if isinstance(array, type(self)) and key is None:
# unwrap
key = array.key # type: ignore[has-type]
array = array.array # type: ignore[has-type]
if key is None:
key = BasicIndexer((slice(None),) * array.ndim)
self.array = as_indexable(array)
self.key = key
shape: _Shape = ()
for size, k in zip(self.array.shape, self.key.tuple, strict=True):
if isinstance(k, slice):
shape += (len(range(*k.indices(size))),)
elif isinstance(k, np.ndarray):
shape += (k.size,)
self._shape = shape
def _updated_key(self, new_key: ExplicitIndexer) -> BasicIndexer | OuterIndexer:
iter_new_key = iter(expanded_indexer(new_key.tuple, self.ndim))
full_key: list[OuterIndexerType] = []
for size, k in zip(self.array.shape, self.key.tuple, strict=True):
if isinstance(k, integer_types):
full_key.append(k)
else:
full_key.append(_index_indexer_1d(k, next(iter_new_key), size))
full_key_tuple = tuple(full_key)
if all(isinstance(k, integer_types + (slice,)) for k in full_key_tuple):
return BasicIndexer(cast(tuple[BasicIndexerType, ...], full_key_tuple))
return OuterIndexer(full_key_tuple)
@property
def shape(self) -> _Shape:
return self._shape
def get_duck_array(self):
from xarray.backends.common import BackendArray
if isinstance(self.array, BackendArray):
array = self.array[self.key]
else:
array = apply_indexer(self.array, self.key)
if isinstance(array, ExplicitlyIndexed):
array = array.get_duck_array()
return _wrap_numpy_scalars(array)
async def async_get_duck_array(self):
from xarray.backends.common import BackendArray
if isinstance(self.array, BackendArray):
array = await self.array.async_getitem(self.key)
else:
array = apply_indexer(self.array, self.key)
if isinstance(array, ExplicitlyIndexed):
array = await array.async_get_duck_array()
return _wrap_numpy_scalars(array)
def transpose(self, order):
return LazilyVectorizedIndexedArray(self.array, self.key).transpose(order)
def _oindex_get(self, indexer: OuterIndexer):
return type(self)(self.array, self._updated_key(indexer))
def _vindex_get(self, indexer: VectorizedIndexer):
array = LazilyVectorizedIndexedArray(self.array, self.key)
return array.vindex[indexer]
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
return type(self)(self.array, self._updated_key(indexer))
def _vindex_set(self, key: VectorizedIndexer, value: Any) -> None:
raise NotImplementedError(
"Lazy item assignment with the vectorized indexer is not yet "
"implemented. Load your data first by .load() or compute()."
)
def _oindex_set(self, key: OuterIndexer, value: Any) -> None:
full_key = self._updated_key(key)
self.array.oindex[full_key] = value
def __setitem__(self, key: BasicIndexer, value: Any) -> None:
self._check_and_raise_if_non_basic_indexer(key)
full_key = self._updated_key(key)
self.array[full_key] = value
def __repr__(self) -> str:
return f"{type(self).__name__}(array={self.array!r}, key={self.key!r})"
# keep an alias to the old name for external backends pydata/xarray#5111
LazilyOuterIndexedArray = LazilyIndexedArray
class LazilyVectorizedIndexedArray(ExplicitlyIndexedNDArrayMixin):
"""Wrap an array to make vectorized indexing lazy."""
__slots__ = ("array", "key")
def __init__(self, array: duckarray[Any, Any], key: ExplicitIndexer):
"""
Parameters
----------
array : array_like
Array like object to index.
key : VectorizedIndexer
"""
if isinstance(key, BasicIndexer | OuterIndexer):
self.key = _outer_to_vectorized_indexer(key, array.shape)
elif isinstance(key, VectorizedIndexer):
self.key = _arrayize_vectorized_indexer(key, array.shape)
self.array = as_indexable(array)
@property
def shape(self) -> _Shape:
return np.broadcast(*self.key.tuple).shape
def get_duck_array(self):
from xarray.backends.common import BackendArray
if isinstance(self.array, BackendArray):
array = self.array[self.key]
else:
array = apply_indexer(self.array, self.key)
if isinstance(array, ExplicitlyIndexed):
array = array.get_duck_array()
return _wrap_numpy_scalars(array)
async def async_get_duck_array(self):
from xarray.backends.common import BackendArray
if isinstance(self.array, BackendArray):
array = await self.array.async_getitem(self.key)
else:
array = apply_indexer(self.array, self.key)
if isinstance(array, ExplicitlyIndexed):
array = await array.async_get_duck_array()
return _wrap_numpy_scalars(array)
def _updated_key(self, new_key: ExplicitIndexer):
return _combine_indexers(self.key, self.shape, new_key)
def _oindex_get(self, indexer: OuterIndexer):
return type(self)(self.array, self._updated_key(indexer))
def _vindex_get(self, indexer: VectorizedIndexer):
return type(self)(self.array, self._updated_key(indexer))
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
# If the indexed array becomes a scalar, return LazilyIndexedArray
if all(isinstance(ind, integer_types) for ind in indexer.tuple):
key = BasicIndexer(tuple(k[indexer.tuple] for k in self.key.tuple))
return LazilyIndexedArray(self.array, key)
return type(self)(self.array, self._updated_key(indexer))
def transpose(self, order):
key = VectorizedIndexer(tuple(k.transpose(order) for k in self.key.tuple))
return type(self)(self.array, key)
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
raise NotImplementedError(
"Lazy item assignment with the vectorized indexer is not yet "
"implemented. Load your data first by .load() or compute()."
)
def __repr__(self) -> str:
return f"{type(self).__name__}(array={self.array!r}, key={self.key!r})"
def _wrap_numpy_scalars(array):
"""Wrap NumPy scalars in 0d arrays."""
ndim = duck_array_ops.ndim(array)
if ndim == 0 and (
isinstance(array, np.generic)
or not (is_duck_array(array) or isinstance(array, NDArrayMixin))
):
return np.array(array)
elif hasattr(array, "dtype"):
return array
elif ndim == 0:
return np.array(array)
else:
return array
class CopyOnWriteArray(ExplicitlyIndexedNDArrayMixin):
__slots__ = ("_copied", "array")
def __init__(self, array: duckarray[Any, Any]):
self.array = as_indexable(array)
self._copied = False
def _ensure_copied(self):
if not self._copied:
self.array = as_indexable(np.array(self.array))
self._copied = True
def get_duck_array(self):
return self.array.get_duck_array()
async def async_get_duck_array(self):
return await self.array.async_get_duck_array()
def _oindex_get(self, indexer: OuterIndexer):
return type(self)(_wrap_numpy_scalars(self.array.oindex[indexer]))
def _vindex_get(self, indexer: VectorizedIndexer):
return type(self)(_wrap_numpy_scalars(self.array.vindex[indexer]))
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
return type(self)(_wrap_numpy_scalars(self.array[indexer]))
def transpose(self, order):
return self.array.transpose(order)
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
self._ensure_copied()
self.array.vindex[indexer] = value
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
self._ensure_copied()
self.array.oindex[indexer] = value
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
self._check_and_raise_if_non_basic_indexer(indexer)
self._ensure_copied()
self.array[indexer] = value
def __deepcopy__(self, memo):
# CopyOnWriteArray is used to wrap backend array objects, which might
# point to files on disk, so we can't rely on the default deepcopy
# implementation.
return type(self)(self.array)
class MemoryCachedArray(ExplicitlyIndexedNDArrayMixin):
__slots__ = ("array",)
def __init__(self, array):
self.array = _wrap_numpy_scalars(as_indexable(array))
def get_duck_array(self):
duck_array = self.array.get_duck_array()
# ensure the array object is cached in-memory
self.array = as_indexable(duck_array)
return duck_array
async def async_get_duck_array(self):
duck_array = await self.array.async_get_duck_array()
# ensure the array object is cached in-memory
self.array = as_indexable(duck_array)
return duck_array
def _oindex_get(self, indexer: OuterIndexer):
return type(self)(_wrap_numpy_scalars(self.array.oindex[indexer]))
def _vindex_get(self, indexer: VectorizedIndexer):
return type(self)(_wrap_numpy_scalars(self.array.vindex[indexer]))
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
return type(self)(_wrap_numpy_scalars(self.array[indexer]))
def transpose(self, order):
return self.array.transpose(order)
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
self.array.vindex[indexer] = value
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
self.array.oindex[indexer] = value
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
self._check_and_raise_if_non_basic_indexer(indexer)
self.array[indexer] = value
def as_indexable(array):
"""
This function always returns a ExplicitlyIndexed subclass,
so that the vectorized indexing is always possible with the returned
object.
"""
if isinstance(array, ExplicitlyIndexed):
return array
if isinstance(array, np.ndarray):
return NumpyIndexingAdapter(array)
if isinstance(array, pd.Index):
return PandasIndexingAdapter(array)
if is_duck_dask_array(array):
return DaskIndexingAdapter(array)
if hasattr(array, "__array_namespace__"):
return ArrayApiIndexingAdapter(array)
if hasattr(array, "__array_function__"):
return NdArrayLikeIndexingAdapter(array)
raise TypeError(f"Invalid array type: {type(array)}")
def _outer_to_vectorized_indexer(
indexer: BasicIndexer | OuterIndexer, shape: _Shape
) -> VectorizedIndexer:
"""Convert an OuterIndexer into an vectorized indexer.
Parameters
----------
indexer : Outer/Basic Indexer
An indexer to convert.
shape : tuple
Shape of the array subject to the indexing.
Returns
-------
VectorizedIndexer
Tuple suitable for use to index a NumPy array with vectorized indexing.
Each element is an array: broadcasting them together gives the shape
of the result.
"""
key = indexer.tuple
n_dim = len([k for k in key if not isinstance(k, integer_types)])
i_dim = 0
new_key = []
for k, size in zip(key, shape, strict=True):
if isinstance(k, integer_types):
new_key.append(np.array(k).reshape((1,) * n_dim))
else: # np.ndarray or slice
if isinstance(k, slice):
k = np.arange(*k.indices(size))
assert k.dtype.kind in {"i", "u"}
new_shape = [(1,) * i_dim + (k.size,) + (1,) * (n_dim - i_dim - 1)]
new_key.append(k.reshape(*new_shape))
i_dim += 1
return VectorizedIndexer(tuple(new_key))
def _outer_to_numpy_indexer(indexer: BasicIndexer | OuterIndexer, shape: _Shape):
"""Convert an OuterIndexer into an indexer for NumPy.
Parameters
----------
indexer : Basic/OuterIndexer
An indexer to convert.
shape : tuple
Shape of the array subject to the indexing.
Returns
-------
tuple
Tuple suitable for use to index a NumPy array.
"""
if len([k for k in indexer.tuple if not isinstance(k, slice)]) <= 1:
# If there is only one vector and all others are slice,
# it can be safely used in mixed basic/advanced indexing.
# Boolean index should already be converted to integer array.
return indexer.tuple
else:
return _outer_to_vectorized_indexer(indexer, shape).tuple
def _combine_indexers(old_key, shape: _Shape, new_key) -> VectorizedIndexer:
"""Combine two indexers.
Parameters
----------
old_key : ExplicitIndexer
The first indexer for the original array
shape : tuple of ints
Shape of the original array to be indexed by old_key
new_key
The second indexer for indexing original[old_key]
"""
if not isinstance(old_key, VectorizedIndexer):
old_key = _outer_to_vectorized_indexer(old_key, shape)
if len(old_key.tuple) == 0:
return new_key
new_shape = np.broadcast(*old_key.tuple).shape
if isinstance(new_key, VectorizedIndexer):
new_key = _arrayize_vectorized_indexer(new_key, new_shape)
else:
new_key = _outer_to_vectorized_indexer(new_key, new_shape)
return VectorizedIndexer(
tuple(o[new_key.tuple] for o in np.broadcast_arrays(*old_key.tuple))
)
@enum.unique
class IndexingSupport(enum.Enum):
# for backends that support only basic indexer
BASIC = 0
# for backends that support basic / outer indexer
OUTER = 1
# for backends that support outer indexer including at most 1 vector.
OUTER_1VECTOR = 2
# for backends that support full vectorized indexer.
VECTORIZED = 3
def explicit_indexing_adapter(
key: ExplicitIndexer,
shape: _Shape,
indexing_support: IndexingSupport,
raw_indexing_method: Callable[..., Any],
) -> Any:
"""Support explicit indexing by delegating to a raw indexing method.
Outer and/or vectorized indexers are supported by indexing a second time
with a NumPy array.
Parameters
----------
key : ExplicitIndexer
Explicit indexing object.
shape : Tuple[int, ...]
Shape of the indexed array.
indexing_support : IndexingSupport enum
Form of indexing supported by raw_indexing_method.
raw_indexing_method : callable
Function (like ndarray.__getitem__) that when called with indexing key
in the form of a tuple returns an indexed array.
Returns
-------
Indexing result, in the form of a duck numpy-array.
"""
raw_key, numpy_indices = decompose_indexer(key, shape, indexing_support)
result = raw_indexing_method(raw_key.tuple)
if numpy_indices.tuple:
# index the loaded duck array
indexable = as_indexable(result)
result = apply_indexer(indexable, numpy_indices)
return result
async def async_explicit_indexing_adapter(
key: ExplicitIndexer,
shape: _Shape,
indexing_support: IndexingSupport,
raw_indexing_method: Callable[..., Any],
) -> Any:
raw_key, numpy_indices = decompose_indexer(key, shape, indexing_support)
result = await raw_indexing_method(raw_key.tuple)
if numpy_indices.tuple:
# index the loaded duck array
indexable = as_indexable(result)
result = apply_indexer(indexable, numpy_indices)
return result
def apply_indexer(indexable, indexer: ExplicitIndexer):
"""Apply an indexer to an indexable object."""
if isinstance(indexer, VectorizedIndexer):
return indexable.vindex[indexer]
elif isinstance(indexer, OuterIndexer):
return indexable.oindex[indexer]
else:
return indexable[indexer]
def set_with_indexer(indexable, indexer: ExplicitIndexer, value: Any) -> None:
"""Set values in an indexable object using an indexer."""
if isinstance(indexer, VectorizedIndexer):
indexable.vindex[indexer] = value
elif isinstance(indexer, OuterIndexer):
indexable.oindex[indexer] = value
else:
indexable[indexer] = value
def decompose_indexer(
indexer: ExplicitIndexer, shape: _Shape, indexing_support: IndexingSupport
) -> tuple[ExplicitIndexer, ExplicitIndexer]:
if isinstance(indexer, VectorizedIndexer):
return _decompose_vectorized_indexer(indexer, shape, indexing_support)
if isinstance(indexer, BasicIndexer | OuterIndexer):
return _decompose_outer_indexer(indexer, shape, indexing_support)
raise TypeError(f"unexpected key type: {indexer}")
def _decompose_slice(key: slice, size: int) -> tuple[slice, slice]:
"""convert a slice to successive two slices. The first slice always has
a positive step.
>>> _decompose_slice(slice(2, 98, 2), 99)
(slice(2, 98, 2), slice(None, None, None))
>>> _decompose_slice(slice(98, 2, -2), 99)
(slice(4, 99, 2), slice(None, None, -1))
>>> _decompose_slice(slice(98, 2, -2), 98)
(slice(3, 98, 2), slice(None, None, -1))
>>> _decompose_slice(slice(360, None, -10), 361)
(slice(0, 361, 10), slice(None, None, -1))
"""
start, stop, step = key.indices(size)
if step > 0:
# If key already has a positive step, use it as is in the backend
return key, slice(None)
else:
# determine stop precisely for step > 1 case
# Use the range object to do the calculation
# e.g. [98:2:-2] -> [98:3:-2]
exact_stop = range(start, stop, step)[-1]
return slice(exact_stop, start + 1, -step), slice(None, None, -1)
def _decompose_vectorized_indexer(
indexer: VectorizedIndexer,
shape: _Shape,
indexing_support: IndexingSupport,
) -> tuple[ExplicitIndexer, ExplicitIndexer]:
"""
Decompose vectorized indexer to the successive two indexers, where the
first indexer will be used to index backend arrays, while the second one
is used to index loaded on-memory np.ndarray.
Parameters
----------
indexer : VectorizedIndexer
indexing_support : one of IndexerSupport entries
Returns
-------
backend_indexer: OuterIndexer or BasicIndexer
np_indexers: an ExplicitIndexer (VectorizedIndexer / BasicIndexer)
Notes
-----
This function is used to realize the vectorized indexing for the backend
arrays that only support basic or outer indexing.
As an example, let us consider to index a few elements from a backend array
with a vectorized indexer ([0, 3, 1], [2, 3, 2]).
Even if the backend array only supports outer indexing, it is more
efficient to load a subslice of the array than loading the entire array,
>>> array = np.arange(36).reshape(6, 6)
>>> backend_indexer = OuterIndexer((np.array([0, 1, 3]), np.array([2, 3])))
>>> # load subslice of the array
... array = NumpyIndexingAdapter(array).oindex[backend_indexer]
>>> np_indexer = VectorizedIndexer((np.array([0, 2, 1]), np.array([0, 1, 0])))
>>> # vectorized indexing for on-memory np.ndarray.
... NumpyIndexingAdapter(array).vindex[np_indexer]
array([ 2, 21, 8])
"""
assert isinstance(indexer, VectorizedIndexer)
if indexing_support is IndexingSupport.VECTORIZED:
return indexer, BasicIndexer(())
backend_indexer_elems = []
np_indexer_elems = []
# convert negative indices
indexer_elems = [
np.where(k < 0, k + s, k) if isinstance(k, np.ndarray) else k
for k, s in zip(indexer.tuple, shape, strict=True)
]
for k, s in zip(indexer_elems, shape, strict=True):
if isinstance(k, slice):
# If it is a slice, then we will slice it as-is
# (but make its step positive) in the backend,
# and then use all of it (slice(None)) for the in-memory portion.
bk_slice, np_slice = _decompose_slice(k, s)
backend_indexer_elems.append(bk_slice)
np_indexer_elems.append(np_slice)
else:
# If it is a (multidimensional) np.ndarray, just pickup the used
# keys without duplication and store them as a 1d-np.ndarray.
oind, vind = np.unique(k, return_inverse=True)
backend_indexer_elems.append(oind)
np_indexer_elems.append(vind.reshape(*k.shape))
backend_indexer = OuterIndexer(tuple(backend_indexer_elems))
np_indexer = VectorizedIndexer(tuple(np_indexer_elems))
if indexing_support is IndexingSupport.OUTER:
return backend_indexer, np_indexer
# If the backend does not support outer indexing,
# backend_indexer (OuterIndexer) is also decomposed.
backend_indexer1, np_indexer1 = _decompose_outer_indexer(
backend_indexer, shape, indexing_support
)
np_indexer = _combine_indexers(np_indexer1, shape, np_indexer)
return backend_indexer1, np_indexer
def _decompose_outer_indexer(
indexer: BasicIndexer | OuterIndexer,
shape: _Shape,
indexing_support: IndexingSupport,
) -> tuple[ExplicitIndexer, ExplicitIndexer]:
"""
Decompose outer indexer to the successive two indexers, where the
first indexer will be used to index backend arrays, while the second one
is used to index the loaded on-memory np.ndarray.
Parameters
----------
indexer : OuterIndexer or BasicIndexer
indexing_support : One of the entries of IndexingSupport
Returns
-------
backend_indexer: OuterIndexer or BasicIndexer
np_indexers: an ExplicitIndexer (OuterIndexer / BasicIndexer)
Notes
-----
This function is used to realize the vectorized indexing for the backend
arrays that only support basic or outer indexing.
As an example, let us consider to index a few elements from a backend array
with a orthogonal indexer ([0, 3, 1], [2, 3, 2]).
Even if the backend array only supports basic indexing, it is more
efficient to load a subslice of the array than loading the entire array,
>>> array = np.arange(36).reshape(6, 6)
>>> backend_indexer = BasicIndexer((slice(0, 3), slice(2, 4)))
>>> # load subslice of the array
... array = NumpyIndexingAdapter(array)[backend_indexer]
>>> np_indexer = OuterIndexer((np.array([0, 2, 1]), np.array([0, 1, 0])))
>>> # outer indexing for on-memory np.ndarray.
... NumpyIndexingAdapter(array).oindex[np_indexer]
array([[ 2, 3, 2],
[14, 15, 14],
[ 8, 9, 8]])
"""
backend_indexer: list[Any] = []
np_indexer: list[Any] = []
assert isinstance(indexer, OuterIndexer | BasicIndexer)
if indexing_support == IndexingSupport.VECTORIZED:
for k, s in zip(indexer.tuple, shape, strict=False):
if isinstance(k, slice):
# If it is a slice, then we will slice it as-is
# (but make its step positive) in the backend,
bk_slice, np_slice = _decompose_slice(k, s)
backend_indexer.append(bk_slice)
np_indexer.append(np_slice)
else:
backend_indexer.append(k)
if not is_scalar(k):
np_indexer.append(slice(None))
return type(indexer)(tuple(backend_indexer)), BasicIndexer(tuple(np_indexer))
# make indexer positive
pos_indexer: list[np.ndarray | int | np.number] = []
for k, s in zip(indexer.tuple, shape, strict=False):
if isinstance(k, np.ndarray):
pos_indexer.append(np.where(k < 0, k + s, k))
elif isinstance(k, integer_types) and k < 0:
pos_indexer.append(k + s)
else:
pos_indexer.append(k)
indexer_elems = pos_indexer
if indexing_support is IndexingSupport.OUTER_1VECTOR:
# some backends such as h5py supports only 1 vector in indexers
# We choose the most efficient axis
gains = [
(
(np.max(k) - np.min(k) + 1.0) / len(np.unique(k))
if isinstance(k, np.ndarray)
else 0
)
for k in indexer_elems
]
array_index = np.argmax(np.array(gains)) if len(gains) > 0 else None
for i, (k, s) in enumerate(zip(indexer_elems, shape, strict=False)):
if isinstance(k, np.ndarray) and i != array_index:
# np.ndarray key is converted to slice that covers the entire
# entries of this key.
backend_indexer.append(slice(np.min(k), np.max(k) + 1))
np_indexer.append(k - np.min(k))
elif isinstance(k, np.ndarray):
# Remove duplicates and sort them in the increasing order
pkey, ekey = np.unique(k, return_inverse=True)
backend_indexer.append(pkey)
np_indexer.append(ekey)
elif isinstance(k, integer_types):
backend_indexer.append(k)
else: # slice: convert positive step slice for backend
bk_slice, np_slice = _decompose_slice(k, s)
backend_indexer.append(bk_slice)
np_indexer.append(np_slice)
return (OuterIndexer(tuple(backend_indexer)), OuterIndexer(tuple(np_indexer)))
if indexing_support == IndexingSupport.OUTER:
for k, s in zip(indexer_elems, shape, strict=False):
if isinstance(k, slice):
# slice: convert positive step slice for backend
bk_slice, np_slice = _decompose_slice(k, s)
backend_indexer.append(bk_slice)
np_indexer.append(np_slice)
elif isinstance(k, integer_types):
backend_indexer.append(k)
elif isinstance(k, np.ndarray) and (np.diff(k) >= 0).all():
backend_indexer.append(k)
np_indexer.append(slice(None))
else:
# Remove duplicates and sort them in the increasing order
oind, vind = np.unique(k, return_inverse=True)
backend_indexer.append(oind)
np_indexer.append(vind.reshape(*k.shape))
return (OuterIndexer(tuple(backend_indexer)), OuterIndexer(tuple(np_indexer)))
# basic indexer
assert indexing_support == IndexingSupport.BASIC
for k, s in zip(indexer_elems, shape, strict=False):
if isinstance(k, np.ndarray):
# np.ndarray key is converted to slice that covers the entire
# entries of this key.
backend_indexer.append(slice(np.min(k), np.max(k) + 1))
np_indexer.append(k - np.min(k))
elif isinstance(k, integer_types):
backend_indexer.append(k)
else: # slice: convert positive step slice for backend
bk_slice, np_slice = _decompose_slice(k, s)
backend_indexer.append(bk_slice)
np_indexer.append(np_slice)
return (BasicIndexer(tuple(backend_indexer)), OuterIndexer(tuple(np_indexer)))
def _posify_indices(indices: Any, size: int) -> np.ndarray:
"""Convert negative indices by their equivalent positive indices.
Note: the resulting indices may still be out of bounds (< 0 or >= size).
"""
return np.where(indices < 0, size + indices, indices)
def _check_bounds(indices: Any, size: int):
"""Check if the given indices are all within the array boundaries."""
if np.any((indices < 0) | (indices >= size)):
raise IndexError("out of bounds index")
def _arrayize_outer_indexer(indexer: OuterIndexer, shape) -> OuterIndexer:
"""Return a similar oindex with after replacing slices by arrays and
negative indices by their corresponding positive indices.
Also check if array indices are within bounds.
"""
new_key = []
for axis, value in enumerate(indexer.tuple):
size = shape[axis]
if isinstance(value, slice):
value = _expand_slice(value, size)
else:
value = _posify_indices(value, size)
_check_bounds(value, size)
new_key.append(value)
return OuterIndexer(tuple(new_key))
def _arrayize_vectorized_indexer(
indexer: VectorizedIndexer, shape: _Shape
) -> VectorizedIndexer:
"""Return an identical vindex but slices are replaced by arrays"""
slices = [v for v in indexer.tuple if isinstance(v, slice)]
if len(slices) == 0:
return indexer
arrays = [v for v in indexer.tuple if isinstance(v, np.ndarray)]
n_dim = arrays[0].ndim if len(arrays) > 0 else 0
i_dim = 0
new_key = []
for v, size in zip(indexer.tuple, shape, strict=True):
if isinstance(v, np.ndarray):
new_key.append(np.reshape(v, v.shape + (1,) * len(slices)))
else: # slice
shape = (1,) * (n_dim + i_dim) + (-1,) + (1,) * (len(slices) - i_dim - 1)
new_key.append(np.arange(*v.indices(size)).reshape(shape))
i_dim += 1
return VectorizedIndexer(tuple(new_key))
def _chunked_array_with_chunks_hint(
array, chunks, chunkmanager: ChunkManagerEntrypoint[Any]
):
"""Create a chunked array using the chunks hint for dimensions of size > 1."""
if len(chunks) < array.ndim:
raise ValueError("not enough chunks in hint")
new_chunks = []
for chunk, size in zip(chunks, array.shape, strict=False):
new_chunks.append(chunk if size > 1 else (1,))
return chunkmanager.from_array(array, new_chunks) # type: ignore[arg-type]
def _logical_any(args):
return functools.reduce(operator.or_, args)
def _masked_result_drop_slice(key, data: duckarray[Any, Any] | None = None):
key = (k for k in key if not isinstance(k, slice))
chunks_hint = getattr(data, "chunks", None)
new_keys = []
for k in key:
if isinstance(k, np.ndarray):
if is_chunked_array(data): # type: ignore[arg-type]
chunkmanager = get_chunked_array_type(data)
new_keys.append(
_chunked_array_with_chunks_hint(k, chunks_hint, chunkmanager)
)
elif isinstance(data, array_type("sparse")):
import sparse
new_keys.append(sparse.COO.from_numpy(k))
else:
new_keys.append(k)
else:
new_keys.append(k)
mask = _logical_any(k == -1 for k in new_keys)
return mask
def create_mask(
indexer: ExplicitIndexer, shape: _Shape, data: duckarray[Any, Any] | None = None
):
"""Create a mask for indexing with a fill-value.
Parameters
----------
indexer : ExplicitIndexer
Indexer with -1 in integer or ndarray value to indicate locations in
the result that should be masked.
shape : tuple
Shape of the array being indexed.
data : optional
Data for which mask is being created. If data is a dask arrays, its chunks
are used as a hint for chunks on the resulting mask. If data is a sparse
array, the returned mask is also a sparse array.
Returns
-------
mask : bool, np.ndarray, SparseArray or dask.array.Array with dtype=bool
Same type as data. Has the same shape as the indexing result.
"""
if isinstance(indexer, OuterIndexer):
key = _outer_to_vectorized_indexer(indexer, shape).tuple
assert not any(isinstance(k, slice) for k in key)
mask = _masked_result_drop_slice(key, data)
elif isinstance(indexer, VectorizedIndexer):
key = indexer.tuple
base_mask = _masked_result_drop_slice(key, data)
slice_shape = tuple(
np.arange(*k.indices(size)).size
for k, size in zip(key, shape, strict=False)
if isinstance(k, slice)
)
expanded_mask = base_mask[(Ellipsis,) + (np.newaxis,) * len(slice_shape)]
mask = duck_array_ops.broadcast_to(expanded_mask, base_mask.shape + slice_shape)
elif isinstance(indexer, BasicIndexer):
mask = any(k == -1 for k in indexer.tuple)
else:
raise TypeError(f"unexpected key type: {type(indexer)}")
return mask
def _posify_mask_subindexer(
index: np.ndarray[Any, np.dtype[np.generic]],
) -> np.ndarray[Any, np.dtype[np.generic]]:
"""Convert masked indices in a flat array to the nearest unmasked index.
Parameters
----------
index : np.ndarray
One dimensional ndarray with dtype=int.
Returns
-------
np.ndarray
One dimensional ndarray with all values equal to -1 replaced by an
adjacent non-masked element.
"""
masked = index == -1
unmasked_locs = np.flatnonzero(~masked)
if not unmasked_locs.size:
# indexing unmasked_locs is invalid
return np.zeros_like(index)
masked_locs = np.flatnonzero(masked)
prev_value = np.maximum(0, np.searchsorted(unmasked_locs, masked_locs) - 1)
new_index = index.copy()
new_index[masked_locs] = index[unmasked_locs[prev_value]]
return new_index
def posify_mask_indexer(indexer: ExplicitIndexer) -> ExplicitIndexer:
"""Convert masked values (-1) in an indexer to nearest unmasked values.
This routine is useful for dask, where it can be much faster to index
adjacent points than arbitrary points from the end of an array.
Parameters
----------
indexer : ExplicitIndexer
Input indexer.
Returns
-------
ExplicitIndexer
Same type of input, with all values in ndarray keys equal to -1
replaced by an adjacent non-masked element.
"""
key = tuple(
(
_posify_mask_subindexer(k.ravel()).reshape(k.shape)
if isinstance(k, np.ndarray)
else k
)
for k in indexer.tuple
)
return type(indexer)(key)
def is_fancy_indexer(indexer: Any) -> bool:
"""Return False if indexer is a int, slice, a 1-dimensional list, or a 0 or
1-dimensional ndarray; in all other cases return True
"""
if isinstance(indexer, int | slice):
return False
if isinstance(indexer, np.ndarray):
return indexer.ndim > 1
if isinstance(indexer, list):
return bool(indexer) and not isinstance(indexer[0], int)
return True
class NumpyIndexingAdapter(IndexingAdapter):
"""Wrap a NumPy array to use explicit indexing."""
__slots__ = ("array",)
def __init__(self, array):
# In NumpyIndexingAdapter we only allow to store bare np.ndarray
if not isinstance(array, np.ndarray):
raise TypeError(
"NumpyIndexingAdapter only wraps np.ndarray. "
f"Trying to wrap {type(array)}"
)
self.array = array
def transpose(self, order):
return self.array.transpose(order)
def _oindex_get(self, indexer: OuterIndexer):
key = _outer_to_numpy_indexer(indexer, self.array.shape)
return self.array[key]
def _vindex_get(self, indexer: VectorizedIndexer):
_assert_not_chunked_indexer(indexer.tuple)
array = NumpyVIndexAdapter(self.array)
return array[indexer.tuple]
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
array = self.array
# We want 0d slices rather than scalars. This is achieved by
# appending an ellipsis (see
# https://numpy.org/doc/stable/reference/arrays.indexing.html#detailed-notes).
key = indexer.tuple + (Ellipsis,)
return array[key]
def _safe_setitem(self, array, key: tuple[Any, ...], value: Any) -> None:
try:
array[key] = value
except ValueError as exc:
# More informative exception if read-only view
if not array.flags.writeable and not array.flags.owndata:
raise ValueError(
"Assignment destination is a view. "
"Do you want to .copy() array first?"
) from exc
else:
raise exc
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
key = _outer_to_numpy_indexer(indexer, self.array.shape)
self._safe_setitem(self.array, key, value)
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
array = NumpyVIndexAdapter(self.array)
self._safe_setitem(array, indexer.tuple, value)
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
self._check_and_raise_if_non_basic_indexer(indexer)
array = self.array
# We want 0d slices rather than scalars. This is achieved by
# appending an ellipsis (see
# https://numpy.org/doc/stable/reference/arrays.indexing.html#detailed-notes).
key = indexer.tuple + (Ellipsis,)
self._safe_setitem(array, key, value)
class NdArrayLikeIndexingAdapter(NumpyIndexingAdapter):
__slots__ = ("array",)
def __init__(self, array):
if not hasattr(array, "__array_function__"):
raise TypeError(
"NdArrayLikeIndexingAdapter must wrap an object that "
"implements the __array_function__ protocol"
)
self.array = array
class ArrayApiIndexingAdapter(IndexingAdapter):
"""Wrap an array API array to use explicit indexing."""
__slots__ = ("array",)
def __init__(self, array):
if not hasattr(array, "__array_namespace__"):
raise TypeError(
"ArrayApiIndexingAdapter must wrap an object that "
"implements the __array_namespace__ protocol"
)
self.array = array
def _oindex_get(self, indexer: OuterIndexer):
# manual orthogonal indexing (implemented like DaskIndexingAdapter)
key = indexer.tuple
value = self.array
for axis, subkey in reversed(list(enumerate(key))):
value = value[(slice(None),) * axis + (subkey, Ellipsis)]
return value
def _vindex_get(self, indexer: VectorizedIndexer):
raise TypeError("Vectorized indexing is not supported")
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
return self.array[indexer.tuple]
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
self.array[indexer.tuple] = value
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
raise TypeError("Vectorized indexing is not supported")
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
self._check_and_raise_if_non_basic_indexer(indexer)
self.array[indexer.tuple] = value
def transpose(self, order):
xp = self.array.__array_namespace__()
return xp.permute_dims(self.array, order)
def _apply_vectorized_indexer_dask_wrapper(indices, coord):
from xarray.core.indexing import (
VectorizedIndexer,
apply_indexer,
as_indexable,
)
return apply_indexer(
as_indexable(coord), VectorizedIndexer((indices.squeeze(axis=-1),))
)
def _assert_not_chunked_indexer(idxr: tuple[Any, ...]) -> None:
if any(is_chunked_array(i) for i in idxr):
raise ValueError(
"Cannot index with a chunked array indexer. "
"Please chunk the array you are indexing first, "
"and drop any indexed dimension coordinate variables. "
"Alternatively, call `.compute()` on any chunked arrays in the indexer."
)
class DaskIndexingAdapter(IndexingAdapter):
"""Wrap a dask array to support explicit indexing."""
__slots__ = ("array",)
def __init__(self, array):
"""This adapter is created in Variable.__getitem__ in
Variable._broadcast_indexes.
"""
self.array = array
def _oindex_get(self, indexer: OuterIndexer):
key = indexer.tuple
try:
return self.array[key]
except NotImplementedError:
# manual orthogonal indexing
value = self.array
for axis, subkey in reversed(list(enumerate(key))):
value = value[(slice(None),) * axis + (subkey,)]
return value
def _vindex_get(self, indexer: VectorizedIndexer):
try:
return self.array.vindex[indexer.tuple]
except IndexError as e:
# TODO: upstream to dask
has_dask = any(is_duck_dask_array(i) for i in indexer.tuple)
# this only works for "small" 1d coordinate arrays with one chunk
# it is intended for idxmin, idxmax, and allows indexing with
# the nD array output of argmin, argmax
if (
not has_dask
or len(indexer.tuple) > 1
or math.prod(self.array.numblocks) > 1
or self.array.ndim > 1
):
raise e
(idxr,) = indexer.tuple
if idxr.ndim == 0:
return self.array[idxr.data]
else:
import dask.array
return dask.array.map_blocks(
_apply_vectorized_indexer_dask_wrapper,
idxr[..., np.newaxis],
self.array,
chunks=idxr.chunks,
drop_axis=-1,
dtype=self.array.dtype,
)
def __getitem__(self, indexer: ExplicitIndexer):
self._check_and_raise_if_non_basic_indexer(indexer)
return self.array[indexer.tuple]
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
num_non_slices = sum(0 if isinstance(k, slice) else 1 for k in indexer.tuple)
if num_non_slices > 1:
raise NotImplementedError(
"xarray can't set arrays with multiple array indices to dask yet."
)
self.array[indexer.tuple] = value
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
self.array.vindex[indexer.tuple] = value
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
self._check_and_raise_if_non_basic_indexer(indexer)
self.array[indexer.tuple] = value
def transpose(self, order):
return self.array.transpose(order)
class PandasIndexingAdapter(IndexingAdapter):
"""Wrap a pandas.Index to preserve dtypes and handle explicit indexing."""
__slots__ = ("_dtype", "array")
array: pd.Index
_dtype: np.dtype | pd.api.extensions.ExtensionDtype
def __init__(
self,
array: pd.Index,
dtype: DTypeLike | pd.api.extensions.ExtensionDtype | None = None,
):
from xarray.core.indexes import safe_cast_to_index
self.array = safe_cast_to_index(array)
if dtype is None:
if is_allowed_extension_array(array):
cast(pd.api.extensions.ExtensionDtype, array.dtype)
self._dtype = array.dtype
else:
self._dtype = get_valid_numpy_dtype(array)
elif is_allowed_extension_array_dtype(dtype):
self._dtype = cast(pd.api.extensions.ExtensionDtype, dtype)
else:
self._dtype = np.dtype(cast(DTypeLike, dtype))
@property
def _in_memory(self) -> bool:
# prevent costly conversion of a memory-saving pd.RangeIndex into a
# large numpy array.
return not isinstance(self.array, pd.RangeIndex)
@property
def dtype(self) -> np.dtype | pd.api.extensions.ExtensionDtype: # type: ignore[override]
return self._dtype
def _get_numpy_dtype(self, dtype: np.typing.DTypeLike | None = None) -> np.dtype:
if dtype is None:
if is_valid_numpy_dtype(self.dtype):
return cast(np.dtype, self.dtype)
else:
return get_valid_numpy_dtype(self.array)
else:
return np.dtype(dtype)
def __array__(
self,
dtype: np.typing.DTypeLike | None = None,
/,
*,
copy: bool | None = None,
) -> np.ndarray:
dtype = self._get_numpy_dtype(dtype)
array = self.array
if isinstance(array, pd.PeriodIndex):
with suppress(AttributeError):
# this might not be public API
array = array.astype("object")
if Version(np.__version__) >= Version("2.0.0"):
return np.asarray(array.values, dtype=dtype, copy=copy)
else:
return np.asarray(array.values, dtype=dtype)
def get_duck_array(self) -> np.ndarray | PandasExtensionArray:
# We return an PandasExtensionArray wrapper type that satisfies
# duck array protocols.
# `NumpyExtensionArray` is excluded
if is_allowed_extension_array(self.array):
from xarray.core.extension_array import PandasExtensionArray
return PandasExtensionArray(self.array.array)
return np.asarray(self)
@property
def shape(self) -> _Shape:
return (len(self.array),)
def _convert_scalar(self, item) -> np.ndarray:
if item is pd.NaT:
# work around the impossibility of casting NaT with asarray
# note: it probably would be better in general to return
# pd.Timestamp rather np.than datetime64 but this is easier
# (for now)
item = np.datetime64("NaT", "ns")
elif isinstance(item, pd.Timedelta):
item = item.to_numpy()
elif isinstance(item, timedelta):
item = np.timedelta64(item)
elif isinstance(item, pd.Timestamp):
# Work around for GH: pydata/xarray#1932 and numpy/numpy#10668
# numpy fails to convert pd.Timestamp to np.datetime64[ns]
item = np.asarray(item.to_datetime64())
elif self.dtype != object:
dtype = self._get_numpy_dtype()
item = np.asarray(item, dtype=dtype)
# as for numpy.ndarray indexing, we always want the result to be
# a NumPy array.
return to_0d_array(item)
def _index_get(
self, indexer: ExplicitIndexer, func_name: str
) -> PandasIndexingAdapter | np.ndarray:
key = indexer.tuple
if len(key) == 1:
# unpack key so it can index a pandas.Index object (pandas.Index
# objects don't like tuples)
(key,) = key
# if multidimensional key, convert the index to numpy array and index the latter
if getattr(key, "ndim", 0) > 1:
indexable = NumpyIndexingAdapter(np.asarray(self))
return getattr(indexable, func_name)(indexer)
# otherwise index the pandas index then re-wrap or convert the result
result = self.array[key]
if isinstance(result, pd.Index):
return type(self)(result, dtype=self.dtype)
else:
return self._convert_scalar(result)
def _oindex_get(self, indexer: OuterIndexer) -> PandasIndexingAdapter | np.ndarray:
return self._index_get(indexer, "_oindex_get")
def _vindex_get(
self, indexer: VectorizedIndexer
) -> PandasIndexingAdapter | np.ndarray:
_assert_not_chunked_indexer(indexer.tuple)
return self._index_get(indexer, "_vindex_get")
def __getitem__(
self, indexer: ExplicitIndexer
) -> PandasIndexingAdapter | np.ndarray:
return self._index_get(indexer, "__getitem__")
def transpose(self, order) -> pd.Index:
return self.array # self.array should be always one-dimensional
def _repr_inline_(self, max_width: int) -> str:
# we want to display values in the inline repr for lazy coordinates too
# (pd.RangeIndex and pd.MultiIndex). `format_array_flat` prevents loading
# the whole array in memory.
from xarray.core.formatting import format_array_flat
return format_array_flat(self, max_width)
def __repr__(self) -> str:
return f"{type(self).__name__}(array={self.array!r}, dtype={self.dtype!r})"
def copy(self, deep: bool = True) -> Self:
# Not the same as just writing `self.array.copy(deep=deep)`, as
# shallow copies of the underlying numpy.ndarrays become deep ones
# upon pickling
# >>> len(pickle.dumps((self.array, self.array)))
# 4000281
# >>> len(pickle.dumps((self.array, self.array.copy(deep=False))))
# 8000341
array = self.array.copy(deep=True) if deep else self.array
return type(self)(array, self._dtype)
@property
def nbytes(self) -> int:
if is_allowed_extension_array(self.array):
return self.array.nbytes
dtype = self._get_numpy_dtype()
return dtype.itemsize * len(self.array)
class PandasMultiIndexingAdapter(PandasIndexingAdapter):
"""Handles explicit indexing for a pandas.MultiIndex.
This allows creating one instance for each multi-index level while
preserving indexing efficiency (memoized + might reuse another instance with
the same multi-index).
"""
__slots__ = ("_dtype", "adapter", "array", "level")
array: pd.MultiIndex
_dtype: np.dtype | pd.api.extensions.ExtensionDtype
level: str | None
def __init__(
self,
array: pd.MultiIndex,
dtype: DTypeLike | pd.api.extensions.ExtensionDtype | None = None,
level: str | None = None,
):
super().__init__(array, dtype)
self.level = level
def __array__(
self,
dtype: DTypeLike | None = None,
/,
*,
copy: bool | None = None,
) -> np.ndarray:
dtype = self._get_numpy_dtype(dtype)
if self.level is not None:
return np.asarray(
self.array.get_level_values(self.level).values, dtype=dtype
)
else:
return super().__array__(dtype, copy=copy)
@property
def _in_memory(self) -> bool:
# The pd.MultiIndex's data is fully in memory, but it has a different
# layout than the level and dimension coordinate arrays. Marking this
# adapter class as a "lazy" array will prevent costly conversion when,
# e.g., formatting the Xarray reprs.
return False
def _convert_scalar(self, item: Any):
if isinstance(item, tuple) and self.level is not None:
idx = tuple(self.array.names).index(self.level)
item = item[idx]
return super()._convert_scalar(item)
def _index_get(
self, indexer: ExplicitIndexer, func_name: str
) -> PandasIndexingAdapter | np.ndarray:
result = super()._index_get(indexer, func_name)
if isinstance(result, type(self)):
result.level = self.level
return result
def __repr__(self) -> str:
if self.level is None:
return super().__repr__()
else:
props = (
f"(array={self.array!r}, level={self.level!r}, dtype={self.dtype!r})"
)
return f"{type(self).__name__}{props}"
def _repr_inline_(self, max_width: int) -> str:
if self.level is None:
return "MultiIndex"
else:
return super()._repr_inline_(max_width=max_width)
def copy(self, deep: bool = True) -> Self:
# see PandasIndexingAdapter.copy
array = self.array.copy(deep=True) if deep else self.array
return type(self)(array, self._dtype, self.level)
class CoordinateTransformIndexingAdapter(IndexingAdapter):
"""Wrap a CoordinateTransform as a lazy coordinate array.
Supports explicit indexing (both outer and vectorized).
"""
_transform: CoordinateTransform
_coord_name: Hashable
_dims: tuple[str, ...]
def __init__(
self,
transform: CoordinateTransform,
coord_name: Hashable,
dims: tuple[str, ...] | None = None,
):
self._transform = transform
self._coord_name = coord_name
self._dims = dims or transform.dims
@property
def dtype(self) -> np.dtype:
return self._transform.dtype
@property
def shape(self) -> tuple[int, ...]:
return tuple(self._transform.dim_size.values())
@property
def _in_memory(self) -> bool:
return False
def get_duck_array(self) -> np.ndarray:
all_coords = self._transform.generate_coords(dims=self._dims)
return np.asarray(all_coords[self._coord_name])
def _oindex_get(self, indexer: OuterIndexer):
expanded_indexer_ = OuterIndexer(expanded_indexer(indexer.tuple, self.ndim))
array_indexer = _arrayize_outer_indexer(expanded_indexer_, self.shape)
positions = np.meshgrid(*array_indexer.tuple, indexing="ij")
dim_positions = dict(zip(self._dims, positions, strict=False))
result = self._transform.forward(dim_positions)
return np.asarray(result[self._coord_name]).squeeze()
def _oindex_set(self, indexer: OuterIndexer, value: Any) -> None:
raise TypeError(
"setting values is not supported on coordinate transform arrays."
)
def _vindex_get(self, indexer: VectorizedIndexer):
expanded_indexer_ = VectorizedIndexer(
expanded_indexer(indexer.tuple, self.ndim)
)
array_indexer = _arrayize_vectorized_indexer(expanded_indexer_, self.shape)
dim_positions = {}
for i, (dim, pos) in enumerate(
zip(self._dims, array_indexer.tuple, strict=False)
):
pos = _posify_indices(pos, self.shape[i])
_check_bounds(pos, self.shape[i])
dim_positions[dim] = pos
result = self._transform.forward(dim_positions)
return np.asarray(result[self._coord_name])
def _vindex_set(self, indexer: VectorizedIndexer, value: Any) -> None:
raise TypeError(
"setting values is not supported on coordinate transform arrays."
)
def __getitem__(self, indexer: ExplicitIndexer):
# TODO: make it lazy (i.e., re-calculate and re-wrap the transform) when possible?
self._check_and_raise_if_non_basic_indexer(indexer)
# also works with basic indexing
return self._oindex_get(OuterIndexer(indexer.tuple))
def __setitem__(self, indexer: ExplicitIndexer, value: Any) -> None:
raise TypeError(
"setting values is not supported on coordinate transform arrays."
)
def transpose(self, order: Iterable[int]) -> Self:
new_dims = tuple(self._dims[i] for i in order)
return type(self)(self._transform, self._coord_name, new_dims)
def __repr__(self: Any) -> str:
return f"{type(self).__name__}(transform={self._transform!r})"
def _repr_inline_(self, max_width: int) -> str:
# we want to display values in the inline repr for this lazy coordinate
# `format_array_flat` prevents loading the whole array in memory.
from xarray.core.formatting import format_array_flat
return format_array_flat(self, max_width)
|