testbed/TileDB-Inc__TileDB-Py/tiledb/array.py

import numpy as np

import tiledb

# Integer types supported by Python / System
_inttypes = (int, np.integer)


def _tiledb_datetime_extent(begin, end):
    """
    Returns the integer extent of a datetime range.

    :param begin: beginning of datetime range
    :type begin: numpy.datetime64
    :param end: end of datetime range
    :type end: numpy.datetime64
    :return: Extent of range, returned as an integer number of time units
    :rtype: int
    """
    extent = end - begin + 1
    date_unit = np.datetime_data(extent.dtype)[0]
    one = np.timedelta64(1, date_unit)
    # Dividing a timedelta by 1 will convert the timedelta to an integer
    return int(extent / one)


def index_as_tuple(idx):
    """Forces scalar index objects to a tuple representation"""
    if isinstance(idx, tuple):
        return idx
    return (idx,)


def replace_ellipsis(ndim: int, idx: tuple):
    """
    Replace indexing ellipsis object with slice objects to match the number
    of dimensions.
    """
    # count number of ellipsis
    n_ellip = sum(1 for i in idx if i is Ellipsis)
    if n_ellip > 1:
        raise IndexError("an index can only have a single ellipsis ('...')")
    elif n_ellip == 1:
        n = len(idx)
        if (n - 1) >= ndim:
            # does nothing, strip it out
            idx = tuple(i for i in idx if i is not Ellipsis)
        else:
            # locate where the ellipse is, count the number of items to left and right
            # fill in whole dim slices up to th ndim of the array
            left = idx.index(Ellipsis)
            right = n - (left + 1)
            new_idx = idx[:left] + ((slice(None),) * (ndim - (n - 1)))
            if right:
                new_idx += idx[-right:]
            idx = new_idx
    idx_ndim = len(idx)
    if idx_ndim < ndim:
        idx += (slice(None),) * (ndim - idx_ndim)
    if len(idx) > ndim:
        raise IndexError("too many indices for array")
    return idx


def replace_scalars_slice(dom, idx: tuple):
    """Replace scalar indices with slice objects"""
    new_idx, drop_axes = [], []
    for i in range(dom.ndim):
        dim = dom.dim(i)
        dim_idx = idx[i]
        if np.isscalar(dim_idx):
            drop_axes.append(i)
            if isinstance(dim_idx, _inttypes):
                start = int(dim_idx)
                if start < 0:
                    start += int(dim.domain[1]) + 1
                stop = start + 1
            else:
                start = dim_idx
                stop = dim_idx
            new_idx.append(slice(start, stop, None))
        else:
            new_idx.append(dim_idx)
    return tuple(new_idx), tuple(drop_axes)


def check_for_floats(selection):
    """
    Check if a selection object contains floating point values

    :param selection: selection object
    :return: True if selection contains floating point values
    :rtype: bool
    """
    if isinstance(selection, float):
        return True
    if isinstance(selection, slice):
        if isinstance(selection.start, float) or isinstance(selection.stop, float):
            return True
    elif isinstance(selection, tuple):
        for s in selection:
            if check_for_floats(s):
                return True
    return False


def index_domain_subarray(array, dom, idx: tuple):
    """
    Return a numpy array representation of the tiledb subarray buffer
    for a given domain and tuple of index slices
    """
    ndim = dom.ndim
    if len(idx) != ndim:
        raise IndexError(
            "number of indices does not match domain rank: "
            "(got {!r}, expected: {!r})".format(len(idx), ndim)
        )

    subarray = list()
    for r in range(ndim):
        # extract lower and upper bounds for domain dimension extent
        dim = dom.dim(r)
        dim_dtype = dim.dtype

        if array.mode == "r" and (
            np.issubdtype(dim_dtype, np.str_) or np.issubdtype(dim_dtype, np.bytes_)
        ):
            # NED can only be retrieved in read mode
            ned = array.nonempty_domain()
            (dim_lb, dim_ub) = ned[r] if ned else (None, None)
        else:
            (dim_lb, dim_ub) = dim.domain

        dim_slice = idx[r]
        if not isinstance(dim_slice, slice):
            raise IndexError("invalid index type: {!r}".format(type(dim_slice)))

        start, stop, step = dim_slice.start, dim_slice.stop, dim_slice.step

        if np.issubdtype(dim_dtype, np.str_) or np.issubdtype(dim_dtype, np.bytes_):
            if start is None or stop is None:
                if start is None:
                    start = dim_lb
                if stop is None:
                    stop = dim_ub
            elif not isinstance(start, (str, bytes)) or not isinstance(
                stop, (str, bytes)
            ):
                raise tiledb.TileDBError(
                    f"Non-string range '({start},{stop})' provided for string dimension '{dim.name}'"
                )
            subarray.append((start, stop))
            continue

        if step and array.schema.sparse:
            raise IndexError("steps are not supported for sparse arrays")

        # Datetimes will be treated specially
        is_datetime = dim_dtype.kind == "M"

        # Promote to a common type
        if start is not None and stop is not None:
            if type(start) != type(stop):
                promoted_dtype = np.promote_types(type(start), type(stop))
                start = np.array(start, dtype=promoted_dtype, ndmin=1)[0]
                stop = np.array(stop, dtype=promoted_dtype, ndmin=1)[0]

        if start is not None:
            if is_datetime and not isinstance(start, np.datetime64):
                raise IndexError(
                    "cannot index datetime dimension with non-datetime interval"
                )
            # don't round / promote fp slices
            if np.issubdtype(dim_dtype, np.integer):
                if isinstance(start, (np.float32, np.float64)):
                    raise IndexError(
                        "cannot index integral domain dimension with floating point slice"
                    )
                elif not isinstance(start, _inttypes):
                    raise IndexError(
                        "cannot index integral domain dimension with non-integral slice (dtype: {})".format(
                            type(start)
                        )
                    )
            # apply negative indexing (wrap-around semantics)
            if not is_datetime and start < 0:
                start += int(dim_ub) + 1
            if start < dim_lb:
                # numpy allows start value < the array dimension shape,
                # clamp to lower bound of dimension domain
                # start = dim_lb
                raise IndexError("index out of bounds <todo>")
        else:
            start = dim_lb
        if stop is not None:
            if is_datetime and not isinstance(stop, np.datetime64):
                raise IndexError(
                    "cannot index datetime dimension with non-datetime interval"
                )
            # don't round / promote fp slices
            if np.issubdtype(dim_dtype, np.integer):
                if isinstance(start, (np.float32, np.float64)):
                    raise IndexError(
                        "cannot index integral domain dimension with floating point slice"
                    )
                elif not isinstance(start, _inttypes):
                    raise IndexError(
                        "cannot index integral domain dimension with non-integral slice (dtype: {})".format(
                            type(start)
                        )
                    )
            if not is_datetime and stop < 0:
                stop = np.int64(stop) + dim_ub
            if stop > dim_ub:
                # numpy allows stop value > than the array dimension shape,
                # clamp to upper bound of dimension domain
                if is_datetime:
                    stop = dim_ub
                else:
                    stop = int(dim_ub) + 1
        else:
            if np.issubdtype(dim_dtype, np.floating) or is_datetime:
                stop = dim_ub
            else:
                stop = int(dim_ub) + 1

        if np.issubdtype(type(stop), np.floating):
            # inclusive bounds for floating point / datetime ranges
            start = dim_dtype.type(start)
            stop = dim_dtype.type(stop)
            subarray.append((start, stop))
        elif is_datetime:
            # need to ensure that datetime ranges are in the units of dim_dtype
            # so that add_range and output shapes work correctly
            start = start.astype(dim_dtype)
            stop = stop.astype(dim_dtype)
            subarray.append((start, stop))
        elif np.issubdtype(type(stop), np.integer):
            # normal python indexing semantics
            subarray.append((start, int(stop) - 1))
        else:
            raise IndexError(
                "domain indexing is defined for integral and floating point values"
            )
    return subarray