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)))