import io import warnings from typing import Any, Optional, Sequence, Union import numpy as np import tiledb.cc as lt from .ctx import Ctx, CtxMixin from .datatypes import DataType from .filter import Filter, FilterList class Attr(CtxMixin, lt.Attribute): """ Represents a TileDB attribute. """ def __init__( self, name: str = "", dtype: np.dtype = np.float64, fill: Any = None, var: bool = None, nullable: bool = False, filters: Union[FilterList, Sequence[Filter]] = None, enum_label: str = None, ctx: Optional[Ctx] = None, ): """Class representing a TileDB array attribute. :param name: Attribute name, empty if anonymous :param dtype: Attribute value datatype :param fill: Fill value for unset cells :param var: Attribute is variable-length (automatic for byte/string types) :param nullable: Attribute is nullable :param filters: List of filters to apply :param ctx: A TileDB Context :raises TypeError: invalid dtype :raises tiledb.TileDBError: """ dt = DataType.from_numpy( np.dtype(dtype) if dtype not in ("ascii", "blob", "wkb", "wkt") else dtype ) # ensure that all strings are var-length if (var is None and dtype == "ascii") or np.issubdtype(dt.np_dtype, np.str_): var = True elif np.issubdtype(dt.np_dtype, np.bytes_): if dt.np_dtype.itemsize > 0 and var: warnings.warn( f"Attr given `var=True` but `dtype` `{dtype}` is fixed; " "setting `dtype=S0`. Hint: set `var=True` with `dtype=S0`, " f"or `var=False`with `dtype={dtype}`", DeprecationWarning, ) elif dt.np_dtype.itemsize == 0 and dtype != "ascii": if var is False: warnings.warn( "Attr given `var=False` but `dtype` `S0` is var-length; " "setting `var=True` and `dtype=S0`. Hint: set `var=False` " "with `dtype=S0`, or `var=False` with a fixed-width " "string `dtype=S` where is n>1", DeprecationWarning, ) var = True super().__init__(ctx, name, dt.tiledb_type) if var: self._ncell = lt.TILEDB_VAR_NUM() elif dt.ncells != lt.TILEDB_VAR_NUM(): self._ncell = dt.ncells else: raise TypeError("dtype is not compatible with var-length attribute") if filters is not None: if isinstance(filters, FilterList): self._filters = filters else: self._filters = FilterList(filters) if fill is not None: if self._tiledb_dtype == lt.DataType.STRING_UTF8: self._fill = np.array([fill.encode("utf-8")], dtype="S") elif self.dtype == np.dtype("complex64") or self.dtype == np.dtype( "complex128" ): if hasattr(fill, "dtype") and fill.dtype in { np.dtype("f4, f4"), np.dtype("f8, f8"), }: _fill = fill["f0"] + fill["f1"] * 1j elif hasattr(fill, "__len__") and len(fill) == 2: _fill = fill[0] + fill[1] * 1j else: _fill = fill self._fill = np.array(_fill, dtype=self.dtype) else: self._fill = np.array([fill], dtype=self.dtype) if nullable is not None: self._nullable = nullable if enum_label is not None: self._set_enumeration_name(self._ctx, enum_label) def __eq__(self, other): if not isinstance(other, Attr): return False if self.isnullable != other.isnullable or self.dtype != other.dtype: return False if not self.isnullable: # Check the fill values are equal. def equal_or_nan(x, y): return x == y or (np.isnan(x) and np.isnan(y)) if self.ncells == 1: if not equal_or_nan(self.fill, other.fill): return False elif np.issubdtype(self.dtype, np.bytes_) or np.issubdtype( self.dtype, np.str_ ): if self.fill != other.fill: return False elif self.dtype in {np.dtype("complex64"), np.dtype("complex128")}: if not ( equal_or_nan(np.real(self.fill), np.real(other.fill)) and equal_or_nan(np.imag(self.fill), np.imag(other.fill)) ): return False else: if not all( equal_or_nan(x, y) or ( isinstance(x, str) and x.lower() == "nat" and isinstance(y, str) and y.lower() == "nat" ) for x, y in zip(self.fill[0], other.fill[0]) ): return False return ( self._internal_name == other._internal_name and self.isvar == other.isvar and self.filters == other.filters ) def dump(self): """Dumps a string representation of the Attr object to standard output (stdout)""" print(self._dump(), "\n") @property def dtype(self) -> np.dtype: """Return numpy dtype object representing the Attr type :rtype: numpy.dtype """ return DataType.from_tiledb(self._tiledb_dtype, self._ncell).np_dtype @property def name(self) -> str: """Attribute string name, empty string if the attribute is anonymous :rtype: str :raises: :py:exc:`tiledb.TileDBError` """ internal_name = self._name # handle __attr names from arrays written with libtiledb < 2 if internal_name == "__attr": return "" return internal_name @property def _internal_name(self): return self._name @property def isanon(self) -> bool: """True if attribute is an anonymous attribute :rtype: bool """ return self._name == "" or self._name.startswith("__attr") @property def filters(self) -> FilterList: """FilterList of the TileDB attribute :rtype: tiledb.FilterList :raises: :py:exc:`tiledb.TileDBError` """ return FilterList.from_pybind11(self._ctx, self._filters) @property def fill(self) -> Any: """Fill value for unset cells of this attribute :rtype: depends on dtype :raises: :py:exc:`tiledb.TileDBERror` """ dtype = self.dtype if np.issubdtype(dtype, np.bytes_): return self._fill.tobytes() if np.issubdtype(dtype, np.str_): return self._fill.tobytes().decode("utf-8") if np.issubdtype(dtype, np.datetime64): return self._fill[0].astype(np.timedelta64) return self._fill @property def isnullable(self) -> bool: """True if the attribute is nullable :rtype: bool :raises: :py:exc:`tiledb.TileDBError` """ return self._nullable @property def isvar(self) -> bool: """True if the attribute is variable length :rtype: bool :raises: :py:exc:`tiledb.TileDBError` """ return self._var @property def ncells(self) -> int: """The number of cells (scalar values) for a given attribute value :rtype: int :raises: :py:exc:`tiledb.TileDBError` """ assert self._ncell != 0 return int(self._ncell) @property def isascii(self) -> bool: """True if the attribute is TileDB dtype TILEDB_STRING_ASCII :rtype: bool :raises: :py:exc:`tiledb.TileDBError` """ return self._tiledb_dtype == lt.DataType.STRING_ASCII @property def enum_label(self): return self._get_enumeration_name(self._ctx) def __repr__(self): # use safe repr if pybind11 constructor failed if self._ctx is None: return object.__repr__(self) filters_str = "" if self.filters: filters_str = ", filters=FilterList([" for f in self.filters: filters_str += repr(f) + ", " filters_str += "])" if self._tiledb_dtype == lt.DataType.STRING_ASCII: attr_dtype = "ascii" elif self._tiledb_dtype == lt.DataType.BLOB: attr_dtype = "blob" elif ( hasattr(lt.DataType, "GEOM_WKB") and self._tiledb_dtype == lt.DataType.GEOM_WKB ): attr_dtype = "wkb" elif ( hasattr(lt.DataType, "GEOM_WKT") and self._tiledb_dtype == lt.DataType.GEOM_WKT ): attr_dtype = "wkt" else: attr_dtype = self.dtype if self.enum_label is None: enum_label = None else: enum_label = f"'{self.enum_label!s}'" # filters_str must be last with no spaces return ( f"""Attr(name={repr(self.name)}, dtype='{attr_dtype!s}', """ f"""var={self.isvar!s}, nullable={self.isnullable!s}, """ f"""enum_label={enum_label}{filters_str})""" ) def _repr_html_(self): output = io.StringIO() output.write("") output.write("") output.write("") output.write("") output.write("") output.write("") output.write("") output.write("") output.write(f"{self._repr_html_row_only_()}") output.write("
NameData TypeIs Var-LenIs NullableFilters
") return output.getvalue() def _repr_html_row_only_(self): output = io.StringIO() output.write("") output.write(f"{self.name}") output.write(f"{'ascii' if self.isascii else self.dtype}") output.write(f"{self.isvar}") output.write(f"{self.isnullable}") output.write(f"{self.filters._repr_html_()}") output.write("") return output.getvalue()