Source code for astropy.nddata.bitmask

"""
A module that provides functions for manipulating bit masks and data quality
(DQ) arrays.

"""
import warnings
import numbers
from collections import OrderedDict
import numpy as np


__all__ = ['bitfield_to_boolean_mask', 'interpret_bit_flags',
           'BitFlagNameMap', 'extend_bit_flag_map', 'InvalidBitFlag']


_ENABLE_BITFLAG_CACHING = True
_MAX_UINT_TYPE = np.maximum_sctype(np.uint)
_SUPPORTED_FLAGS = int(np.bitwise_not(
    0, dtype=_MAX_UINT_TYPE, casting='unsafe'
))


def _is_bit_flag(n):
    """
    Verifies if the input number is a bit flag (i.e., an integer number that is
    an integer power of 2).

    Parameters
    ----------
    n : int
        A positive integer number. Non-positive integers are considered not to
        be "flags".

    Returns
    -------
    bool
        ``True`` if input ``n`` is a bit flag and ``False`` if it is not.

    """
    if n < 1:
        return False

    return bin(n).count('1') == 1


def _is_int(n):
    return (
        (isinstance(n, numbers.Integral) and not isinstance(n, bool)) or
        (isinstance(n, np.generic) and np.issubdtype(n, np.integer))
    )


[docs]class InvalidBitFlag(ValueError): """ Indicates that a value is not an integer that is a power of 2. """ pass
class BitFlag(int): """ Bit flags: integer values that are powers of 2. """ def __new__(cls, val, doc=None): if isinstance(val, tuple): if doc is not None: raise ValueError("Flag's doc string cannot be provided twice.") val, doc = val if not (_is_int(val) and _is_bit_flag(val)): raise InvalidBitFlag( "Value '{}' is not a valid bit flag: bit flag value must be " "an integral power of two.".format(val) ) s = int.__new__(cls, val) if doc is not None: s.__doc__ = doc return s class BitFlagNameMeta(type): def __new__(mcls, name, bases, members): for k, v in members.items(): if not k.startswith('_'): v = BitFlag(v) attr = [k for k in members.keys() if not k.startswith('_')] attrl = list(map(str.lower, attr)) if _ENABLE_BITFLAG_CACHING: cache = OrderedDict() for b in bases: for k, v in b.__dict__.items(): if k.startswith('_'): continue kl = k.lower() if kl in attrl: idx = attrl.index(kl) raise AttributeError("Bit flag '{:s}' was already defined." .format(attr[idx])) if _ENABLE_BITFLAG_CACHING: cache[kl] = v members = {k: v if k.startswith('_') else BitFlag(v) for k, v in members.items()} if _ENABLE_BITFLAG_CACHING: cache.update({k.lower(): v for k, v in members.items() if not k.startswith('_')}) members = {'_locked': True, '__version__': '', **members, '_cache': cache} else: members = {'_locked': True, '__version__': '', **members} return super().__new__(mcls, name, bases, members) def __setattr__(cls, name, val): if name == '_locked': return super().__setattr__(name, True) else: if name == '__version__': if cls._locked: raise AttributeError("Version cannot be modified.") return super().__setattr__(name, val) err_msg = "Bit flags are read-only. Unable to reassign attribute {}".format(name) if cls._locked: raise AttributeError(err_msg) namel = name.lower() if _ENABLE_BITFLAG_CACHING: if not namel.startswith('_') and namel in cls._cache: raise AttributeError(err_msg) else: for b in cls.__bases__: if not namel.startswith('_') and namel in list(map(str.lower, b.__dict__)): raise AttributeError(err_msg) if namel in list(map(str.lower, cls.__dict__)): raise AttributeError(err_msg) val = BitFlag(val) if _ENABLE_BITFLAG_CACHING and not namel.startswith('_'): cls._cache[namel] = val return super().__setattr__(name, val) def __getattr__(cls, name): if _ENABLE_BITFLAG_CACHING: flagnames = cls._cache else: flagnames = {k.lower(): v for k, v in cls.__dict__.items()} flagnames.update({k.lower(): v for b in cls.__bases__ for k, v in b.__dict__.items()}) try: return flagnames[name.lower()] except KeyError: raise AttributeError("Flag '{}' not defined".format(name)) def __getitem__(cls, key): return cls.__getattr__(key) def __add__(cls, items): if not isinstance(items, dict): if not isinstance(items[0], (tuple, list)): items = [items] items = dict(items) return extend_bit_flag_map( cls.__name__ + '_' + '_'.join([k for k in items]), cls, **items ) def __iadd__(cls, other): raise NotImplementedError( "Unary '+' is not supported. Use binary operator instead." ) def __delattr__(cls, name): raise AttributeError("{:s}: cannot delete {:s} member." .format(cls.__name__, cls.mro()[-2].__name__)) def __delitem__(cls, name): raise AttributeError("{:s}: cannot delete {:s} member." .format(cls.__name__, cls.mro()[-2].__name__)) def __repr__(cls): return "<{:s} '{:s}'>".format(cls.mro()[-2].__name__, cls.__name__)
[docs]class BitFlagNameMap(metaclass=BitFlagNameMeta): """ A base class for bit flag name maps used to describe data quality (DQ) flags of images by provinding a mapping from a mnemonic flag name to a flag value. Mapping for a specific instrument should subclass this class. Subclasses should define flags as class attributes with integer values that are powers of 2. Each bit flag may also contain a string comment following the flag value. Examples -------- >>> from astropy.nddata.bitmask import BitFlagNameMap >>> class ST_DQ(BitFlagNameMap): ... __version__ = '1.0.0' # optional ... CR = 1, 'Cosmic Ray' ... CLOUDY = 4 # no docstring comment ... RAINY = 8, 'Dome closed' ... >>> class ST_CAM1_DQ(ST_DQ): ... HOT = 16 ... DEAD = 32 """ pass
[docs]def extend_bit_flag_map(cls_name, base_cls=BitFlagNameMap, **kwargs): """ A convenience function for creating bit flags maps by subclassing an existing map and adding additional flags supplied as keyword arguments. Parameters ---------- cls_name : str Class name of the bit flag map to be created. base_cls : BitFlagNameMap, optional Base class for the new bit flag map. **kwargs : int Each supplied keyword argument will be used to define bit flag names in the new map. In addition to bit flag names, ``__version__`` is allowed to indicate the version of the newly created map. Examples -------- >>> from astropy.nddata.bitmask import extend_bit_flag_map >>> ST_DQ = extend_bit_flag_map('ST_DQ', __version__='1.0.0', CR=1, CLOUDY=4, RAINY=8) >>> ST_CAM1_DQ = extend_bit_flag_map('ST_CAM1_DQ', ST_DQ, HOT=16, DEAD=32) >>> ST_CAM1_DQ['HOT'] # <-- Access flags as dictionary keys 16 >>> ST_CAM1_DQ.HOT # <-- Access flags as class attributes 16 """ new_cls = BitFlagNameMeta.__new__( BitFlagNameMeta, cls_name, (base_cls, ), {'_locked': False} ) for k, v in kwargs.items(): try: setattr(new_cls, k, v) except AttributeError as e: if new_cls[k] != int(v): raise e new_cls._locked = True return new_cls
[docs]def interpret_bit_flags(bit_flags, flip_bits=None, flag_name_map=None): """ Converts input bit flags to a single integer value (bit mask) or `None`. When input is a list of flags (either a Python list of integer flags or a string of comma-, ``'|'``-, or ``'+'``-separated list of flags), the returned bit mask is obtained by summing input flags. .. note:: In order to flip the bits of the returned bit mask, for input of `str` type, prepend '~' to the input string. '~' must be prepended to the *entire string* and not to each bit flag! For input that is already a bit mask or a Python list of bit flags, set ``flip_bits`` for `True` in order to flip the bits of the returned bit mask. Parameters ---------- bit_flags : int, str, list, None An integer bit mask or flag, `None`, a string of comma-, ``'|'``- or ``'+'``-separated list of integer bit flags or mnemonic flag names, or a Python list of integer bit flags. If ``bit_flags`` is a `str` and if it is prepended with '~', then the output bit mask will have its bits flipped (compared to simple sum of input flags). For input ``bit_flags`` that is already a bit mask or a Python list of bit flags, bit-flipping can be controlled through ``flip_bits`` parameter. .. note:: When ``bit_flags`` is a list of flag names, the ``flag_name_map`` parameter must be provided. .. note:: Only one flag separator is supported at a time. ``bit_flags`` string should not mix ``','``, ``'+'``, and ``'|'`` separators. flip_bits : bool, None Indicates whether or not to flip the bits of the returned bit mask obtained from input bit flags. This parameter must be set to `None` when input ``bit_flags`` is either `None` or a Python list of flags. flag_name_map : BitFlagNameMap A `BitFlagNameMap` object that provides mapping from mnemonic bit flag names to integer bit values in order to translate mnemonic flags to numeric values when ``bit_flags`` that are comma- or '+'-separated list of menmonic bit flag names. Returns ------- bitmask : int or None Returns an integer bit mask formed from the input bit value or `None` if input ``bit_flags`` parameter is `None` or an empty string. If input string value was prepended with '~' (or ``flip_bits`` was set to `True`), then returned value will have its bits flipped (inverse mask). Examples -------- >>> from astropy.nddata.bitmask import interpret_bit_flags, extend_bit_flag_map >>> ST_DQ = extend_bit_flag_map('ST_DQ', CR=1, CLOUDY=4, RAINY=8, HOT=16, DEAD=32) >>> "{0:016b}".format(0xFFFF & interpret_bit_flags(28)) '0000000000011100' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags('4,8,16')) '0000000000011100' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags('CLOUDY,RAINY,HOT', flag_name_map=ST_DQ)) '0000000000011100' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags('~4,8,16')) '1111111111100011' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags('~(4+8+16)')) '1111111111100011' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags('~(CLOUDY+RAINY+HOT)', ... flag_name_map=ST_DQ)) '1111111111100011' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags([4, 8, 16])) '0000000000011100' >>> "{0:016b}".format(0xFFFF & interpret_bit_flags([4, 8, 16], flip_bits=True)) '1111111111100011' """ has_flip_bits = flip_bits is not None flip_bits = bool(flip_bits) allow_non_flags = False if _is_int(bit_flags): return (~int(bit_flags) if flip_bits else int(bit_flags)) elif bit_flags is None: if has_flip_bits: raise TypeError( "Keyword argument 'flip_bits' must be set to 'None' when " "input 'bit_flags' is None." ) return None elif isinstance(bit_flags, str): if has_flip_bits: raise TypeError( "Keyword argument 'flip_bits' is not permitted for " "comma-separated string lists of bit flags. Prepend '~' to " "the string to indicate bit-flipping." ) bit_flags = str(bit_flags).strip() if bit_flags.upper() in ['', 'NONE', 'INDEF']: return None # check whether bitwise-NOT is present and if it is, check that it is # in the first position: bitflip_pos = bit_flags.find('~') if bitflip_pos == 0: flip_bits = True bit_flags = bit_flags[1:].lstrip() else: if bitflip_pos > 0: raise ValueError("Bitwise-NOT must precede bit flag list.") flip_bits = False # basic check for correct use of parenthesis: while True: nlpar = bit_flags.count('(') nrpar = bit_flags.count(')') if nlpar == 0 and nrpar == 0: break if nlpar != nrpar: raise ValueError("Unbalanced parantheses in bit flag list.") lpar_pos = bit_flags.find('(') rpar_pos = bit_flags.rfind(')') if lpar_pos > 0 or rpar_pos < (len(bit_flags) - 1): raise ValueError("Incorrect syntax (incorrect use of " "parenthesis) in bit flag list.") bit_flags = bit_flags[1:-1].strip() if sum(k in bit_flags for k in '+,|') > 1: raise ValueError( "Only one type of bit flag separator may be used in one " "expression. Allowed separators are: '+', '|', or ','." ) if ',' in bit_flags: bit_flags = bit_flags.split(',') elif '+' in bit_flags: bit_flags = bit_flags.split('+') elif '|' in bit_flags: bit_flags = bit_flags.split('|') else: if bit_flags == '': raise ValueError( "Empty bit flag lists not allowed when either bitwise-NOT " "or parenthesis are present." ) bit_flags = [bit_flags] if flag_name_map is not None: try: int(bit_flags[0]) except ValueError: bit_flags = [flag_name_map[f] for f in bit_flags] allow_non_flags = len(bit_flags) == 1 elif hasattr(bit_flags, '__iter__'): if not all([_is_int(flag) for flag in bit_flags]): if (flag_name_map is not None and all([isinstance(flag, str) for flag in bit_flags])): bit_flags = [flag_name_map[f] for f in bit_flags] else: raise TypeError("Every bit flag in a list must be either an " "integer flag value or a 'str' flag name.") else: raise TypeError("Unsupported type for argument 'bit_flags'.") bitset = set(map(int, bit_flags)) if len(bitset) != len(bit_flags): warnings.warn("Duplicate bit flags will be ignored") bitmask = 0 for v in bitset: if not _is_bit_flag(v) and not allow_non_flags: raise ValueError("Input list contains invalid (not powers of two) " "bit flag: {:d}".format(v)) bitmask += v if flip_bits: bitmask = ~bitmask return bitmask
[docs]def bitfield_to_boolean_mask(bitfield, ignore_flags=0, flip_bits=None, good_mask_value=False, dtype=np.bool_, flag_name_map=None): """ bitfield_to_boolean_mask(bitfield, ignore_flags=None, flip_bits=None, \ good_mask_value=False, dtype=numpy.bool_) Converts an array of bit fields to a boolean (or integer) mask array according to a bit mask constructed from the supplied bit flags (see ``ignore_flags`` parameter). This function is particularly useful to convert data quality arrays to boolean masks with selective filtering of DQ flags. Parameters ---------- bitfield : numpy.ndarray An array of bit flags. By default, values different from zero are interpreted as "bad" values and values equal to zero are considered as "good" values. However, see ``ignore_flags`` parameter on how to selectively ignore some bits in the ``bitfield`` array data. ignore_flags : int, str, list, None (Default = 0) An integer bit mask, `None`, a Python list of bit flags, a comma-, or ``'|'``-separated, ``'+'``-separated string list of integer bit flags or mnemonic flag names that indicate what bits in the input ``bitfield`` should be *ignored* (i.e., zeroed), or `None`. .. note:: When ``bit_flags`` is a list of flag names, the ``flag_name_map`` parameter must be provided. | Setting ``ignore_flags`` to `None` effectively will make `bitfield_to_boolean_mask` interpret all ``bitfield`` elements as "good" regardless of their value. | When ``ignore_flags`` argument is an integer bit mask, it will be combined using bitwise-NOT and bitwise-AND with each element of the input ``bitfield`` array (``~ignore_flags & bitfield``). If the resultant bitfield element is non-zero, that element will be interpreted as a "bad" in the output boolean mask and it will be interpreted as "good" otherwise. ``flip_bits`` parameter may be used to flip the bits (``bitwise-NOT``) of the bit mask thus effectively changing the meaning of the ``ignore_flags`` parameter from "ignore" to "use only" these flags. .. note:: Setting ``ignore_flags`` to 0 effectively will assume that all non-zero elements in the input ``bitfield`` array are to be interpreted as "bad". | When ``ignore_flags`` argument is a Python list of integer bit flags, these flags are added together to create an integer bit mask. Each item in the list must be a flag, i.e., an integer that is an integer power of 2. In order to flip the bits of the resultant bit mask, use ``flip_bits`` parameter. | Alternatively, ``ignore_flags`` may be a string of comma- or ``'+'``(or ``'|'``)-separated list of integer bit flags that should be added (bitwise OR) together to create an integer bit mask. For example, both ``'4,8'``, ``'4|8'``, and ``'4+8'`` are equivalent and indicate that bit flags 4 and 8 in the input ``bitfield`` array should be ignored when generating boolean mask. .. note:: ``'None'``, ``'INDEF'``, and empty (or all white space) strings are special values of string ``ignore_flags`` that are interpreted as `None`. .. note:: Each item in the list must be a flag, i.e., an integer that is an integer power of 2. In addition, for convenience, an arbitrary **single** integer is allowed and it will be interpretted as an integer bit mask. For example, instead of ``'4,8'`` one could simply provide string ``'12'``. .. note:: Only one flag separator is supported at a time. ``ignore_flags`` string should not mix ``','``, ``'+'``, and ``'|'`` separators. .. note:: When ``ignore_flags`` is a `str` and when it is prepended with '~', then the meaning of ``ignore_flags`` parameters will be reversed: now it will be interpreted as a list of bit flags to be *used* (or *not ignored*) when deciding which elements of the input ``bitfield`` array are "bad". Following this convention, an ``ignore_flags`` string value of ``'~0'`` would be equivalent to setting ``ignore_flags=None``. .. warning:: Because prepending '~' to a string ``ignore_flags`` is equivalent to setting ``flip_bits`` to `True`, ``flip_bits`` cannot be used with string ``ignore_flags`` and it must be set to `None`. flip_bits : bool, None (Default = None) Specifies whether or not to invert the bits of the bit mask either supplied directly through ``ignore_flags`` parameter or built from the bit flags passed through ``ignore_flags`` (only when bit flags are passed as Python lists of integer bit flags). Occasionally, it may be useful to *consider only specific bit flags* in the ``bitfield`` array when creating a boolean mask as opposed to *ignoring* specific bit flags as ``ignore_flags`` behaves by default. This can be achieved by inverting/flipping the bits of the bit mask created from ``ignore_flags`` flags which effectively changes the meaning of the ``ignore_flags`` parameter from "ignore" to "use only" these flags. Setting ``flip_bits`` to `None` means that no bit flipping will be performed. Bit flipping for string lists of bit flags must be specified by prepending '~' to string bit flag lists (see documentation for ``ignore_flags`` for more details). .. warning:: This parameter can be set to either `True` or `False` **ONLY** when ``ignore_flags`` is either an integer bit mask or a Python list of integer bit flags. When ``ignore_flags`` is either `None` or a string list of flags, ``flip_bits`` **MUST** be set to `None`. good_mask_value : int, bool (Default = False) This parameter is used to derive the values that will be assigned to the elements in the output boolean mask array that correspond to the "good" bit fields (that are 0 after zeroing bits specified by ``ignore_flags``) in the input ``bitfield`` array. When ``good_mask_value`` is non-zero or ``numpy.True_`` then values in the output boolean mask array corresponding to "good" bit fields in ``bitfield`` will be ``numpy.True_`` (if ``dtype`` is ``numpy.bool_``) or 1 (if ``dtype`` is of numerical type) and values of corresponding to "bad" flags will be ``numpy.False_`` (or 0). When ``good_mask_value`` is zero or ``numpy.False_`` then the values in the output boolean mask array corresponding to "good" bit fields in ``bitfield`` will be ``numpy.False_`` (if ``dtype`` is ``numpy.bool_``) or 0 (if ``dtype`` is of numerical type) and values of corresponding to "bad" flags will be ``numpy.True_`` (or 1). dtype : data-type (Default = ``numpy.bool_``) The desired data-type for the output binary mask array. flag_name_map : BitFlagNameMap A `BitFlagNameMap` object that provides mapping from mnemonic bit flag names to integer bit values in order to translate mnemonic flags to numeric values when ``bit_flags`` that are comma- or '+'-separated list of menmonic bit flag names. Returns ------- mask : numpy.ndarray Returns an array of the same dimensionality as the input ``bitfield`` array whose elements can have two possible values, e.g., ``numpy.True_`` or ``numpy.False_`` (or 1 or 0 for integer ``dtype``) according to values of to the input ``bitfield`` elements, ``ignore_flags`` parameter, and the ``good_mask_value`` parameter. Examples -------- >>> from astropy.nddata import bitmask >>> import numpy as np >>> dqarr = np.asarray([[0, 0, 1, 2, 0, 8, 12, 0], ... [10, 4, 0, 0, 0, 16, 6, 0]]) >>> flag_map = bitmask.extend_bit_flag_map( ... 'ST_DQ', CR=2, CLOUDY=4, RAINY=8, HOT=16, DEAD=32 ... ) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags=0, ... dtype=int) array([[0, 0, 1, 1, 0, 1, 1, 0], [1, 1, 0, 0, 0, 1, 1, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags=0, ... dtype=bool) array([[False, False, True, True, False, True, True, False], [ True, True, False, False, False, True, True, False]]...) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags=6, ... good_mask_value=0, dtype=int) array([[0, 0, 1, 0, 0, 1, 1, 0], [1, 0, 0, 0, 0, 1, 0, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags=~6, ... good_mask_value=0, dtype=int) array([[0, 0, 0, 1, 0, 0, 1, 0], [1, 1, 0, 0, 0, 0, 1, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags=6, dtype=int, ... flip_bits=True, good_mask_value=0) array([[0, 0, 0, 1, 0, 0, 1, 0], [1, 1, 0, 0, 0, 0, 1, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags='~(2+4)', ... good_mask_value=0, dtype=int) array([[0, 0, 0, 1, 0, 0, 1, 0], [1, 1, 0, 0, 0, 0, 1, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags=[2, 4], ... flip_bits=True, good_mask_value=0, ... dtype=int) array([[0, 0, 0, 1, 0, 0, 1, 0], [1, 1, 0, 0, 0, 0, 1, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags='~(CR,CLOUDY)', ... good_mask_value=0, dtype=int, ... flag_name_map=flag_map) array([[0, 0, 0, 1, 0, 0, 1, 0], [1, 1, 0, 0, 0, 0, 1, 0]]) >>> bitmask.bitfield_to_boolean_mask(dqarr, ignore_flags='~(CR+CLOUDY)', ... good_mask_value=0, dtype=int, ... flag_name_map=flag_map) array([[0, 0, 0, 1, 0, 0, 1, 0], [1, 1, 0, 0, 0, 0, 1, 0]]) """ bitfield = np.asarray(bitfield) if not np.issubdtype(bitfield.dtype, np.integer): raise TypeError("Input bitfield array must be of integer type.") ignore_mask = interpret_bit_flags(ignore_flags, flip_bits=flip_bits, flag_name_map=flag_name_map) if ignore_mask is None: if good_mask_value: mask = np.ones_like(bitfield, dtype=dtype) else: mask = np.zeros_like(bitfield, dtype=dtype) return mask # filter out bits beyond the maximum supported by the data type: ignore_mask = ignore_mask & _SUPPORTED_FLAGS # invert the "ignore" mask: ignore_mask = np.bitwise_not(ignore_mask, dtype=bitfield.dtype, casting='unsafe') mask = np.empty_like(bitfield, dtype=np.bool_) np.bitwise_and(bitfield, ignore_mask, out=mask, casting='unsafe') if good_mask_value: np.logical_not(mask, out=mask) return mask.astype(dtype=dtype, subok=False, copy=False)