File size: 3,931 Bytes
2c3c408 | 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 | import weakref
import numpy as np
import tiledb
import tiledb.cc as lt
def _index_as_tuple(idx):
"""Forces scalar index objects to a tuple representation"""
if isinstance(idx, tuple):
return idx
return (idx,)
class DomainIndexer:
@staticmethod
def with_schema(schema):
indexer = DomainIndexer.__new__(DomainIndexer)
indexer.array = None
indexer.schema = schema
return indexer
def __init__(self, array, query=None):
self.array_ref = weakref.ref(array)
self.schema = array.schema
self.query = query
# @property
def schema(self):
return self.array.array_ref().schema
@property
def array(self):
assert (
self.array_ref() is not None
), "Internal error: invariant violation (index[] with dead array_ref)"
return self.array_ref()
def __getitem__(self, idx):
from .subarray import Subarray # prevent circular import
# implements domain-based indexing: slice by domain coordinates, not 0-based python indexing
schema = self.array.schema
dom = schema.domain
ndim = dom.ndim
attr_names = list()
idx = _index_as_tuple(idx)
if len(idx) < dom.ndim:
raise IndexError(
"number of indices does not match domain rank: "
"(got {!r}, expected: {!r})".format(len(idx), ndim)
)
new_idx = []
for i in range(dom.ndim):
dim = dom.dim(i)
dim_idx = idx[i]
if np.isscalar(dim_idx):
start = dim_idx
stop = dim_idx
new_idx.append(slice(start, stop, None))
else:
new_idx.append(dim_idx)
dim_ranges = list()
for i, subidx in enumerate(new_idx):
assert isinstance(subidx, slice)
dim_ranges.append((subidx.start, subidx.stop))
subarray = Subarray(self.array)
subarray.add_ranges([list([x]) for x in dim_ranges])
attr_names = list(schema.attr(i).name for i in range(schema.nattr))
attr_cond = None
order = None
# TODO make coords optional for array.domain_index. there are no kwargs in slicing[], so
# one way to do this would be to overload __call__ and return a new
# object with a flag set. not ideal.
coords = True
if self.query is not None:
# if we are called via Query object, then we need to respect Query semantics
order = self.query.order
attr_names = (
self.query.attrs if self.query.attrs else attr_names
) # query.attrs might be None -> all
attr_cond = self.query.attr_cond
coords = self.query.coords
if coords:
attr_names = [
dom.dim(idx).name for idx in range(self.schema.ndim)
] + attr_names
if order is None or order == "C":
layout = lt.LayoutType.ROW_MAJOR
elif order == "F":
layout = lt.LayoutType.COL_MAJOR
elif order == "G":
layout = lt.LayoutType.GLOBAL_ORDER
elif order == "U":
layout = lt.LayoutType.UNORDERED
else:
raise ValueError(
"order must be 'C' (TILEDB_ROW_MAJOR), 'F' (TILEDB_COL_MAJOR), or 'G' (TILEDB_GLOBAL_ORDER)"
)
if isinstance(self.array, tiledb.sparse_array.SparseArrayImpl):
return self.array._read_sparse_subarray(
subarray, attr_names, attr_cond, layout
)
elif isinstance(self.array, tiledb.dense_array.DenseArrayImpl):
return self.array._read_dense_subarray(
subarray, attr_names, attr_cond, layout, coords
)
else:
raise Exception("No handler for Array type: " + str(type(self.array)))
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