Source code for astropy.io.fits.column

# Licensed under a 3-clause BSD style license - see PYFITS.rst

import copy
import operator
import re
import sys
import warnings
import weakref
import numbers

from functools import reduce
from collections import OrderedDict
from contextlib import suppress

import numpy as np
from numpy import char as chararray

from .card import Card, CARD_LENGTH
from .util import (pairwise, _is_int, _convert_array, encode_ascii, cmp,
                   NotifierMixin)
from .verify import VerifyError, VerifyWarning

from astropy.utils import lazyproperty, isiterable, indent
from astropy.utils.exceptions import AstropyUserWarning

__all__ = ['Column', 'ColDefs', 'Delayed']


# mapping from TFORM data type to numpy data type (code)
# L: Logical (Boolean)
# B: Unsigned Byte
# I: 16-bit Integer
# J: 32-bit Integer
# K: 64-bit Integer
# E: Single-precision Floating Point
# D: Double-precision Floating Point
# C: Single-precision Complex
# M: Double-precision Complex
# A: Character
FITS2NUMPY = {'L': 'i1', 'B': 'u1', 'I': 'i2', 'J': 'i4', 'K': 'i8', 'E': 'f4',
              'D': 'f8', 'C': 'c8', 'M': 'c16', 'A': 'a'}

# the inverse dictionary of the above
NUMPY2FITS = {val: key for key, val in FITS2NUMPY.items()}
# Normally booleans are represented as ints in Astropy, but if passed in a numpy
# boolean array, that should be supported
NUMPY2FITS['b1'] = 'L'
# Add unsigned types, which will be stored as signed ints with a TZERO card.
NUMPY2FITS['u2'] = 'I'
NUMPY2FITS['u4'] = 'J'
NUMPY2FITS['u8'] = 'K'
# Add half precision floating point numbers which will be up-converted to
# single precision.
NUMPY2FITS['f2'] = 'E'

# This is the order in which values are converted to FITS types
# Note that only double precision floating point/complex are supported
FORMATORDER = ['L', 'B', 'I', 'J', 'K', 'D', 'M', 'A']

# Convert single precision floating point/complex to double precision.
FITSUPCONVERTERS = {'E': 'D', 'C': 'M'}

# mapping from ASCII table TFORM data type to numpy data type
# A: Character
# I: Integer (32-bit)
# J: Integer (64-bit; non-standard)
# F: Float (64-bit; fixed decimal notation)
# E: Float (64-bit; exponential notation)
# D: Float (64-bit; exponential notation, always 64-bit by convention)
ASCII2NUMPY = {'A': 'a', 'I': 'i4', 'J': 'i8', 'F': 'f8', 'E': 'f8', 'D': 'f8'}

# Maps FITS ASCII column format codes to the appropriate Python string
# formatting codes for that type.
ASCII2STR = {'A': '', 'I': 'd', 'J': 'd', 'F': 'f', 'E': 'E', 'D': 'E'}

# For each ASCII table format code, provides a default width (and decimal
# precision) for when one isn't given explicitly in the column format
ASCII_DEFAULT_WIDTHS = {'A': (1, 0), 'I': (10, 0), 'J': (15, 0),
                        'E': (15, 7), 'F': (16, 7), 'D': (25, 17)}

# TDISPn for both ASCII and Binary tables
TDISP_RE_DICT = {}
TDISP_RE_DICT['F'] = re.compile(r'(?:(?P<formatc>[F])(?:(?P<width>[0-9]+)\.{1}'
                                r'(?P<precision>[0-9])+)+)|')
TDISP_RE_DICT['A'] = TDISP_RE_DICT['L'] = \
    re.compile(r'(?:(?P<formatc>[AL])(?P<width>[0-9]+)+)|')
TDISP_RE_DICT['I'] = TDISP_RE_DICT['B'] = \
    TDISP_RE_DICT['O'] = TDISP_RE_DICT['Z'] =  \
    re.compile(r'(?:(?P<formatc>[IBOZ])(?:(?P<width>[0-9]+)'
               r'(?:\.{0,1}(?P<precision>[0-9]+))?))|')
TDISP_RE_DICT['E'] = TDISP_RE_DICT['G'] = \
    TDISP_RE_DICT['D'] = \
    re.compile(r'(?:(?P<formatc>[EGD])(?:(?P<width>[0-9]+)\.'
               r'(?P<precision>[0-9]+))+)'
               r'(?:E{0,1}(?P<exponential>[0-9]+)?)|')
TDISP_RE_DICT['EN'] = TDISP_RE_DICT['ES'] = \
    re.compile(r'(?:(?P<formatc>E[NS])(?:(?P<width>[0-9]+)\.{1}'
               r'(?P<precision>[0-9])+)+)')

# mapping from TDISP format to python format
# A: Character
# L: Logical (Boolean)
# I: 16-bit Integer
#    Can't predefine zero padding and space padding before hand without
#    knowing the value being formatted, so grabbing precision and using that
#    to zero pad, ignoring width. Same with B, O, and Z
# B: Binary Integer
# O: Octal Integer
# Z: Hexadecimal Integer
# F: Float (64-bit; fixed decimal notation)
# EN: Float (engineering fortran format, exponential multiple of thee
# ES: Float (scientific, same as EN but non-zero leading digit
# E: Float, exponential notation
#    Can't get exponential restriction to work without knowing value
#    before hand, so just using width and precision, same with D, G, EN, and
#    ES formats
# D: Double-precision Floating Point with exponential
#    (E but for double precision)
# G: Double-precision Floating Point, may or may not show exponent
TDISP_FMT_DICT = {'I' : '{{:{width}d}}',
                  'B' : '{{:{width}b}}',
                  'O' : '{{:{width}o}}',
                  'Z' : '{{:{width}x}}',
                  'F' : '{{:{width}.{precision}f}}',
                  'G' : '{{:{width}.{precision}g}}'}
TDISP_FMT_DICT['A'] = TDISP_FMT_DICT['L'] = '{{:>{width}}}'
TDISP_FMT_DICT['E'] = TDISP_FMT_DICT['D'] =  \
    TDISP_FMT_DICT['EN'] = TDISP_FMT_DICT['ES'] ='{{:{width}.{precision}e}}'

# tuple of column/field definition common names and keyword names, make
# sure to preserve the one-to-one correspondence when updating the list(s).
# Use lists, instead of dictionaries so the names can be displayed in a
# preferred order.
KEYWORD_NAMES = ('TTYPE', 'TFORM', 'TUNIT', 'TNULL', 'TSCAL', 'TZERO',
                 'TDISP', 'TBCOL', 'TDIM', 'TCTYP', 'TCUNI', 'TCRPX',
                 'TCRVL', 'TCDLT', 'TRPOS')
KEYWORD_ATTRIBUTES = ('name', 'format', 'unit', 'null', 'bscale', 'bzero',
                      'disp', 'start', 'dim', 'coord_type', 'coord_unit',
                      'coord_ref_point', 'coord_ref_value', 'coord_inc',
                      'time_ref_pos')
"""This is a list of the attributes that can be set on `Column` objects."""


KEYWORD_TO_ATTRIBUTE = OrderedDict(zip(KEYWORD_NAMES, KEYWORD_ATTRIBUTES))

ATTRIBUTE_TO_KEYWORD = OrderedDict(zip(KEYWORD_ATTRIBUTES, KEYWORD_NAMES))


# TODO: Define a list of default comments to associate with each table keyword

# TFORMn regular expression
TFORMAT_RE = re.compile(r'(?P<repeat>^[0-9]*)(?P<format>[LXBIJKAEDCMPQ])'
                        r'(?P<option>[!-~]*)', re.I)

# TFORMn for ASCII tables; two different versions depending on whether
# the format is floating-point or not; allows empty values for width
# in which case defaults are used
TFORMAT_ASCII_RE = re.compile(r'(?:(?P<format>[AIJ])(?P<width>[0-9]+)?)|'
                              r'(?:(?P<formatf>[FED])'
                              r'(?:(?P<widthf>[0-9]+)\.'
                              r'(?P<precision>[0-9]+))?)')

TTYPE_RE = re.compile(r'[0-9a-zA-Z_]+')
"""
Regular expression for valid table column names.  See FITS Standard v3.0 section
7.2.2.
"""

# table definition keyword regular expression
TDEF_RE = re.compile(r'(?P<label>^T[A-Z]*)(?P<num>[1-9][0-9 ]*$)')

# table dimension keyword regular expression (fairly flexible with whitespace)
TDIM_RE = re.compile(r'\(\s*(?P<dims>(?:\d+,\s*)+\s*\d+)\s*\)\s*')

# value for ASCII table cell with value = TNULL
# this can be reset by user.
ASCIITNULL = 0

# The default placeholder to use for NULL values in ASCII tables when
# converting from binary to ASCII tables
DEFAULT_ASCII_TNULL = '---'


class Delayed:
    """Delayed file-reading data."""

    def __init__(self, hdu=None, field=None):
        self.hdu = weakref.proxy(hdu)
        self.field = field

    def __getitem__(self, key):
        # This forces the data for the HDU to be read, which will replace
        # the corresponding Delayed objects in the Tables Columns to be
        # transformed into ndarrays.  It will also return the value of the
        # requested data element.
        return self.hdu.data[key][self.field]


class _BaseColumnFormat(str):
    """
    Base class for binary table column formats (just called _ColumnFormat)
    and ASCII table column formats (_AsciiColumnFormat).
    """

    def __eq__(self, other):
        if not other:
            return False

        if isinstance(other, str):
            if not isinstance(other, self.__class__):
                try:
                    other = self.__class__(other)
                except ValueError:
                    return False
        else:
            return False

        return self.canonical == other.canonical

    def __hash__(self):
        return hash(self.canonical)

    @lazyproperty
    def dtype(self):
        """
        The Numpy dtype object created from the format's associated recformat.
        """

        return np.dtype(self.recformat)

    @classmethod
    def from_column_format(cls, format):
        """Creates a column format object from another column format object
        regardless of their type.

        That is, this can convert a _ColumnFormat to an _AsciiColumnFormat
        or vice versa at least in cases where a direct translation is possible.
        """

        return cls.from_recformat(format.recformat)


class _ColumnFormat(_BaseColumnFormat):
    """
    Represents a FITS binary table column format.

    This is an enhancement over using a normal string for the format, since the
    repeat count, format code, and option are available as separate attributes,
    and smart comparison is used.  For example 1J == J.
    """

    def __new__(cls, format):
        self = super().__new__(cls, format)
        self.repeat, self.format, self.option = _parse_tformat(format)
        self.format = self.format.upper()
        if self.format in ('P', 'Q'):
            # TODO: There should be a generic factory that returns either
            # _FormatP or _FormatQ as appropriate for a given TFORMn
            if self.format == 'P':
                recformat = _FormatP.from_tform(format)
            else:
                recformat = _FormatQ.from_tform(format)
            # Format of variable length arrays
            self.p_format = recformat.format
        else:
            self.p_format = None
        return self

    @classmethod
    def from_recformat(cls, recformat):
        """Creates a column format from a Numpy record dtype format."""

        return cls(_convert_format(recformat, reverse=True))

    @lazyproperty
    def recformat(self):
        """Returns the equivalent Numpy record format string."""

        return _convert_format(self)

    @lazyproperty
    def canonical(self):
        """
        Returns a 'canonical' string representation of this format.

        This is in the proper form of rTa where T is the single character data
        type code, a is the optional part, and r is the repeat.  If repeat == 1
        (the default) it is left out of this representation.
        """

        if self.repeat == 1:
            repeat = ''
        else:
            repeat = str(self.repeat)

        return f'{repeat}{self.format}{self.option}'


class _AsciiColumnFormat(_BaseColumnFormat):
    """Similar to _ColumnFormat but specifically for columns in ASCII tables.

    The formats of ASCII table columns and binary table columns are inherently
    incompatible in FITS.  They don't support the same ranges and types of
    values, and even reuse format codes in subtly different ways.  For example
    the format code 'Iw' in ASCII columns refers to any integer whose string
    representation is at most w characters wide, so 'I' can represent
    effectively any integer that will fit in a FITS columns.  Whereas for
    binary tables 'I' very explicitly refers to a 16-bit signed integer.

    Conversions between the two column formats can be performed using the
    ``to/from_binary`` methods on this class, or the ``to/from_ascii``
    methods on the `_ColumnFormat` class.  But again, not all conversions are
    possible and may result in a `ValueError`.
    """

    def __new__(cls, format, strict=False):
        self = super().__new__(cls, format)
        self.format, self.width, self.precision = \
            _parse_ascii_tformat(format, strict)

        # This is to support handling logical (boolean) data from binary tables
        # in an ASCII table
        self._pseudo_logical = False
        return self

    @classmethod
    def from_column_format(cls, format):
        inst = cls.from_recformat(format.recformat)
        # Hack
        if format.format == 'L':
            inst._pseudo_logical = True
        return inst

    @classmethod
    def from_recformat(cls, recformat):
        """Creates a column format from a Numpy record dtype format."""

        return cls(_convert_ascii_format(recformat, reverse=True))

    @lazyproperty
    def recformat(self):
        """Returns the equivalent Numpy record format string."""

        return _convert_ascii_format(self)

    @lazyproperty
    def canonical(self):
        """
        Returns a 'canonical' string representation of this format.

        This is in the proper form of Tw.d where T is the single character data
        type code, w is the width in characters for this field, and d is the
        number of digits after the decimal place (for format codes 'E', 'F',
        and 'D' only).
        """

        if self.format in ('E', 'F', 'D'):
            return f'{self.format}{self.width}.{self.precision}'

        return f'{self.format}{self.width}'


class _FormatX(str):
    """For X format in binary tables."""

    def __new__(cls, repeat=1):
        nbytes = ((repeat - 1) // 8) + 1
        # use an array, even if it is only ONE u1 (i.e. use tuple always)
        obj = super().__new__(cls, repr((nbytes,)) + 'u1')
        obj.repeat = repeat
        return obj

    def __getnewargs__(self):
        return (self.repeat,)

    @property
    def tform(self):
        return f'{self.repeat}X'


# TODO: Table column formats need to be verified upon first reading the file;
# as it is, an invalid P format will raise a VerifyError from some deep,
# unexpected place
class _FormatP(str):
    """For P format in variable length table."""

    # As far as I can tell from my reading of the FITS standard, a type code is
    # *required* for P and Q formats; there is no default
    _format_re_template = (r'(?P<repeat>\d+)?{}(?P<dtype>[LXBIJKAEDCM])'
                           r'(?:\((?P<max>\d*)\))?')
    _format_code = 'P'
    _format_re = re.compile(_format_re_template.format(_format_code))
    _descriptor_format = '2i4'

    def __new__(cls, dtype, repeat=None, max=None):
        obj = super().__new__(cls, cls._descriptor_format)
        obj.format = NUMPY2FITS[dtype]
        obj.dtype = dtype
        obj.repeat = repeat
        obj.max = max
        return obj

    def __getnewargs__(self):
        return (self.dtype, self.repeat, self.max)

    @classmethod
    def from_tform(cls, format):
        m = cls._format_re.match(format)
        if not m or m.group('dtype') not in FITS2NUMPY:
            raise VerifyError(f'Invalid column format: {format}')
        repeat = m.group('repeat')
        array_dtype = m.group('dtype')
        max = m.group('max')
        if not max:
            max = None
        return cls(FITS2NUMPY[array_dtype], repeat=repeat, max=max)

    @property
    def tform(self):
        repeat = '' if self.repeat is None else self.repeat
        max = '' if self.max is None else self.max
        return f'{repeat}{self._format_code}{self.format}({max})'


class _FormatQ(_FormatP):
    """Carries type description of the Q format for variable length arrays.

    The Q format is like the P format but uses 64-bit integers in the array
    descriptors, allowing for heaps stored beyond 2GB into a file.
    """

    _format_code = 'Q'
    _format_re = re.compile(_FormatP._format_re_template.format(_format_code))
    _descriptor_format = '2i8'


class ColumnAttribute:
    """
    Descriptor for attributes of `Column` that are associated with keywords
    in the FITS header and describe properties of the column as specified in
    the FITS standard.

    Each `ColumnAttribute` may have a ``validator`` method defined on it.
    This validates values set on this attribute to ensure that they meet the
    FITS standard.  Invalid values will raise a warning and will not be used in
    formatting the column.  The validator should take two arguments--the
    `Column` it is being assigned to, and the new value for the attribute, and
    it must raise an `AssertionError` if the value is invalid.

    The `ColumnAttribute` itself is a decorator that can be used to define the
    ``validator`` for each column attribute.  For example::

        @ColumnAttribute('TTYPE')
        def name(col, name):
            if not isinstance(name, str):
                raise AssertionError

    The actual object returned by this decorator is the `ColumnAttribute`
    instance though, not the ``name`` function.  As such ``name`` is not a
    method of the class it is defined in.

    The setter for `ColumnAttribute` also updates the header of any table
    HDU this column is attached to in order to reflect the change.  The
    ``validator`` should ensure that the value is valid for inclusion in a FITS
    header.
    """

    def __init__(self, keyword):
        self._keyword = keyword
        self._validator = None

        # The name of the attribute associated with this keyword is currently
        # determined from the KEYWORD_NAMES/ATTRIBUTES lists.  This could be
        # make more flexible in the future, for example, to support custom
        # column attributes.
        self._attr = '_' + KEYWORD_TO_ATTRIBUTE[self._keyword]

    def __get__(self, obj, objtype=None):
        if obj is None:
            return self
        else:
            return getattr(obj, self._attr)

    def __set__(self, obj, value):
        if self._validator is not None:
            self._validator(obj, value)

        old_value = getattr(obj, self._attr, None)
        setattr(obj, self._attr, value)
        obj._notify('column_attribute_changed', obj, self._attr[1:], old_value,
                    value)

    def __call__(self, func):
        """
        Set the validator for this column attribute.

        Returns ``self`` so that this can be used as a decorator, as described
        in the docs for this class.
        """

        self._validator = func

        return self

    def __repr__(self):
        return f"{self.__class__.__name__}('{self._keyword}')"


[docs]class Column(NotifierMixin): """ Class which contains the definition of one column, e.g. ``ttype``, ``tform``, etc. and the array containing values for the column. """ def __init__(self, name=None, format=None, unit=None, null=None, bscale=None, bzero=None, disp=None, start=None, dim=None, array=None, ascii=None, coord_type=None, coord_unit=None, coord_ref_point=None, coord_ref_value=None, coord_inc=None, time_ref_pos=None): """ Construct a `Column` by specifying attributes. All attributes except ``format`` can be optional; see :ref:`column_creation` and :ref:`creating_ascii_table` for more information regarding ``TFORM`` keyword. Parameters ---------- name : str, optional column name, corresponding to ``TTYPE`` keyword format : str column format, corresponding to ``TFORM`` keyword unit : str, optional column unit, corresponding to ``TUNIT`` keyword null : str, optional null value, corresponding to ``TNULL`` keyword bscale : int-like, optional bscale value, corresponding to ``TSCAL`` keyword bzero : int-like, optional bzero value, corresponding to ``TZERO`` keyword disp : str, optional display format, corresponding to ``TDISP`` keyword start : int, optional column starting position (ASCII table only), corresponding to ``TBCOL`` keyword dim : str, optional column dimension corresponding to ``TDIM`` keyword array : iterable, optional a `list`, `numpy.ndarray` (or other iterable that can be used to initialize an ndarray) providing initial data for this column. The array will be automatically converted, if possible, to the data format of the column. In the case were non-trivial ``bscale`` and/or ``bzero`` arguments are given, the values in the array must be the *physical* values--that is, the values of column as if the scaling has already been applied (the array stored on the column object will then be converted back to its storage values). ascii : bool, optional set `True` if this describes a column for an ASCII table; this may be required to disambiguate the column format coord_type : str, optional coordinate/axis type corresponding to ``TCTYP`` keyword coord_unit : str, optional coordinate/axis unit corresponding to ``TCUNI`` keyword coord_ref_point : int-like, optional pixel coordinate of the reference point corresponding to ``TCRPX`` keyword coord_ref_value : int-like, optional coordinate value at reference point corresponding to ``TCRVL`` keyword coord_inc : int-like, optional coordinate increment at reference point corresponding to ``TCDLT`` keyword time_ref_pos : str, optional reference position for a time coordinate column corresponding to ``TRPOS`` keyword """ if format is None: raise ValueError('Must specify format to construct Column.') # any of the input argument (except array) can be a Card or just # a number/string kwargs = {'ascii': ascii} for attr in KEYWORD_ATTRIBUTES: value = locals()[attr] # get the argument's value if isinstance(value, Card): value = value.value kwargs[attr] = value valid_kwargs, invalid_kwargs = self._verify_keywords(**kwargs) if invalid_kwargs: msg = ['The following keyword arguments to Column were invalid:'] for val in invalid_kwargs.values(): msg.append(indent(val[1])) raise VerifyError('\n'.join(msg)) for attr in KEYWORD_ATTRIBUTES: setattr(self, attr, valid_kwargs.get(attr)) # TODO: Try to eliminate the following two special cases # for recformat and dim: # This is not actually stored as an attribute on columns for some # reason recformat = valid_kwargs['recformat'] # The 'dim' keyword's original value is stored in self.dim, while # *only* the tuple form is stored in self._dims. self._dims = self.dim self.dim = dim # Awful hack to use for now to keep track of whether the column holds # pseudo-unsigned int data self._pseudo_unsigned_ints = False # if the column data is not ndarray, make it to be one, i.e. # input arrays can be just list or tuple, not required to be ndarray # does not include Object array because there is no guarantee # the elements in the object array are consistent. if not isinstance(array, (np.ndarray, chararray.chararray, Delayed)): try: # try to convert to a ndarray first if array is not None: array = np.array(array) except Exception: try: # then try to convert it to a strings array itemsize = int(recformat[1:]) array = chararray.array(array, itemsize=itemsize) except ValueError: # then try variable length array # Note: This includes _FormatQ by inheritance if isinstance(recformat, _FormatP): array = _VLF(array, dtype=recformat.dtype) else: raise ValueError('Data is inconsistent with the ' 'format `{}`.'.format(format)) array = self._convert_to_valid_data_type(array) # We have required (through documentation) that arrays passed in to # this constructor are already in their physical values, so we make # note of that here if isinstance(array, np.ndarray): self._physical_values = True else: self._physical_values = False self._parent_fits_rec = None self.array = array def __repr__(self): text = '' for attr in KEYWORD_ATTRIBUTES: value = getattr(self, attr) if value is not None: text += attr + ' = ' + repr(value) + '; ' return text[:-2] def __eq__(self, other): """ Two columns are equal if their name and format are the same. Other attributes aren't taken into account at this time. """ # According to the FITS standard column names must be case-insensitive a = (self.name.lower(), self.format) b = (other.name.lower(), other.format) return a == b def __hash__(self): """ Like __eq__, the hash of a column should be based on the unique column name and format, and be case-insensitive with respect to the column name. """ return hash((self.name.lower(), self.format)) @property def array(self): """ The Numpy `~numpy.ndarray` associated with this `Column`. If the column was instantiated with an array passed to the ``array`` argument, this will return that array. However, if the column is later added to a table, such as via `BinTableHDU.from_columns` as is typically the case, this attribute will be updated to reference the associated field in the table, which may no longer be the same array. """ # Ideally the .array attribute never would have existed in the first # place, or would have been internal-only. This is a legacy of the # older design from Astropy that needs to have continued support, for # now. # One of the main problems with this design was that it created a # reference cycle. When the .array attribute was updated after # creating a FITS_rec from the column (as explained in the docstring) a # reference cycle was created. This is because the code in BinTableHDU # (and a few other places) does essentially the following: # # data._coldefs = columns # The ColDefs object holding this Column # for col in columns: # col.array = data.field(col.name) # # This way each columns .array attribute now points to the field in the # table data. It's actually a pretty confusing interface (since it # replaces the array originally pointed to by .array), but it's the way # things have been for a long, long time. # # However, this results, in *many* cases, in a reference cycle. # Because the array returned by data.field(col.name), while sometimes # an array that owns its own data, is usually like a slice of the # original data. It has the original FITS_rec as the array .base. # This results in the following reference cycle (for the n-th column): # # data -> data._coldefs -> data._coldefs[n] -> # data._coldefs[n].array -> data._coldefs[n].array.base -> data # # Because ndarray objects do not handled by Python's garbage collector # the reference cycle cannot be broken. Therefore the FITS_rec's # refcount never goes to zero, its __del__ is never called, and its # memory is never freed. This didn't occur in *all* cases, but it did # occur in many cases. # # To get around this, Column.array is no longer a simple attribute # like it was previously. Now each Column has a ._parent_fits_rec # attribute which is a weakref to a FITS_rec object. Code that # previously assigned each col.array to field in a FITS_rec (as in # the example a few paragraphs above) is still used, however now # array.setter checks if a reference cycle will be created. And if # so, instead of saving directly to the Column's __dict__, it creates # the ._prent_fits_rec weakref, and all lookups of the column's .array # go through that instead. # # This alone does not fully solve the problem. Because # _parent_fits_rec is a weakref, if the user ever holds a reference to # the Column, but deletes all references to the underlying FITS_rec, # the .array attribute would suddenly start returning None instead of # the array data. This problem is resolved on FITS_rec's end. See the # note in the FITS_rec._coldefs property for the rest of the story. # If the Columns's array is not a reference to an existing FITS_rec, # then it is just stored in self.__dict__; otherwise check the # _parent_fits_rec reference if it 's still available. if 'array' in self.__dict__: return self.__dict__['array'] elif self._parent_fits_rec is not None: parent = self._parent_fits_rec() if parent is not None: return parent[self.name] else: return None @array.setter def array(self, array): # The following looks over the bases of the given array to check if it # has a ._coldefs attribute (i.e. is a FITS_rec) and that that _coldefs # contains this Column itself, and would create a reference cycle if we # stored the array directly in self.__dict__. # In this case it instead sets up the _parent_fits_rec weakref to the # underlying FITS_rec, so that array.getter can return arrays through # self._parent_fits_rec().field(self.name), rather than storing a # hard reference to the field like it used to. base = array while True: if (hasattr(base, '_coldefs') and isinstance(base._coldefs, ColDefs)): for col in base._coldefs: if col is self and self._parent_fits_rec is None: self._parent_fits_rec = weakref.ref(base) # Just in case the user already set .array to their own # array. if 'array' in self.__dict__: del self.__dict__['array'] return if getattr(base, 'base', None) is not None: base = base.base else: break self.__dict__['array'] = array @array.deleter def array(self): try: del self.__dict__['array'] except KeyError: pass self._parent_fits_rec = None @ColumnAttribute('TTYPE') def name(col, name): if name is None: # Allow None to indicate deleting the name, or to just indicate an # unspecified name (when creating a new Column). return # Check that the name meets the recommended standard--other column # names are *allowed*, but will be discouraged if isinstance(name, str) and not TTYPE_RE.match(name): warnings.warn( 'It is strongly recommended that column names contain only ' 'upper and lower-case ASCII letters, digits, or underscores ' 'for maximum compatibility with other software ' '(got {!r}).'.format(name), VerifyWarning) # This ensures that the new name can fit into a single FITS card # without any special extension like CONTINUE cards or the like. if (not isinstance(name, str) or len(str(Card('TTYPE', name))) != CARD_LENGTH): raise AssertionError( 'Column name must be a string able to fit in a single ' 'FITS card--typically this means a maximum of 68 ' 'characters, though it may be fewer if the string ' 'contains special characters like quotes.') @ColumnAttribute('TCTYP') def coord_type(col, coord_type): if coord_type is None: return if (not isinstance(coord_type, str) or len(coord_type) > 8): raise AssertionError( 'Coordinate/axis type must be a string of atmost 8 ' 'characters.') @ColumnAttribute('TCUNI') def coord_unit(col, coord_unit): if (coord_unit is not None and not isinstance(coord_unit, str)): raise AssertionError( 'Coordinate/axis unit must be a string.') @ColumnAttribute('TCRPX') def coord_ref_point(col, coord_ref_point): if (coord_ref_point is not None and not isinstance(coord_ref_point, numbers.Real)): raise AssertionError( 'Pixel coordinate of the reference point must be ' 'real floating type.') @ColumnAttribute('TCRVL') def coord_ref_value(col, coord_ref_value): if (coord_ref_value is not None and not isinstance(coord_ref_value, numbers.Real)): raise AssertionError( 'Coordinate value at reference point must be real ' 'floating type.') @ColumnAttribute('TCDLT') def coord_inc(col, coord_inc): if (coord_inc is not None and not isinstance(coord_inc, numbers.Real)): raise AssertionError( 'Coordinate increment must be real floating type.') @ColumnAttribute('TRPOS') def time_ref_pos(col, time_ref_pos): if (time_ref_pos is not None and not isinstance(time_ref_pos, str)): raise AssertionError( 'Time reference position must be a string.') format = ColumnAttribute('TFORM') unit = ColumnAttribute('TUNIT') null = ColumnAttribute('TNULL') bscale = ColumnAttribute('TSCAL') bzero = ColumnAttribute('TZERO') disp = ColumnAttribute('TDISP') start = ColumnAttribute('TBCOL') dim = ColumnAttribute('TDIM') @lazyproperty def ascii(self): """Whether this `Column` represents a column in an ASCII table.""" return isinstance(self.format, _AsciiColumnFormat) @lazyproperty def dtype(self): return self.format.dtype
[docs] def copy(self): """ Return a copy of this `Column`. """ tmp = Column(format='I') # just use a throw-away format tmp.__dict__ = self.__dict__.copy() return tmp
@staticmethod def _convert_format(format, cls): """The format argument to this class's initializer may come in many forms. This uses the given column format class ``cls`` to convert to a format of that type. TODO: There should be an abc base class for column format classes """ # Short circuit in case we're already a _BaseColumnFormat--there is at # least one case in which this can happen if isinstance(format, _BaseColumnFormat): return format, format.recformat if format in NUMPY2FITS: with suppress(VerifyError): # legit recarray format? recformat = format format = cls.from_recformat(format) try: # legit FITS format? format = cls(format) recformat = format.recformat except VerifyError: raise VerifyError(f'Illegal format `{format}`.') return format, recformat @classmethod def _verify_keywords(cls, name=None, format=None, unit=None, null=None, bscale=None, bzero=None, disp=None, start=None, dim=None, ascii=None, coord_type=None, coord_unit=None, coord_ref_point=None, coord_ref_value=None, coord_inc=None, time_ref_pos=None): """ Given the keyword arguments used to initialize a Column, specifically those that typically read from a FITS header (so excluding array), verify that each keyword has a valid value. Returns a 2-tuple of dicts. The first maps valid keywords to their values. The second maps invalid keywords to a 2-tuple of their value, and a message explaining why they were found invalid. """ valid = {} invalid = {} format, recformat = cls._determine_formats(format, start, dim, ascii) valid.update(format=format, recformat=recformat) # Currently we don't have any validation for name, unit, bscale, or # bzero so include those by default # TODO: Add validation for these keywords, obviously for k, v in [('name', name), ('unit', unit), ('bscale', bscale), ('bzero', bzero)]: if v is not None and v != '': valid[k] = v # Validate null option # Note: Enough code exists that thinks empty strings are sensible # inputs for these options that we need to treat '' as None if null is not None and null != '': msg = None if isinstance(format, _AsciiColumnFormat): null = str(null) if len(null) > format.width: msg = ( "ASCII table null option (TNULLn) is longer than " "the column's character width and will be truncated " "(got {!r}).".format(null)) else: tnull_formats = ('B', 'I', 'J', 'K') if not _is_int(null): # Make this an exception instead of a warning, since any # non-int value is meaningless msg = ( 'Column null option (TNULLn) must be an integer for ' 'binary table columns (got {!r}). The invalid value ' 'will be ignored for the purpose of formatting ' 'the data in this column.'.format(null)) elif not (format.format in tnull_formats or (format.format in ('P', 'Q') and format.p_format in tnull_formats)): # TODO: We should also check that TNULLn's integer value # is in the range allowed by the column's format msg = ( 'Column null option (TNULLn) is invalid for binary ' 'table columns of type {!r} (got {!r}). The invalid ' 'value will be ignored for the purpose of formatting ' 'the data in this column.'.format(format, null)) if msg is None: valid['null'] = null else: invalid['null'] = (null, msg) # Validate the disp option # TODO: Add full parsing and validation of TDISPn keywords if disp is not None and disp != '': msg = None if not isinstance(disp, str): msg = ( 'Column disp option (TDISPn) must be a string (got {!r}).' 'The invalid value will be ignored for the purpose of ' 'formatting the data in this column.'.format(disp)) elif (isinstance(format, _AsciiColumnFormat) and disp[0].upper() == 'L'): # disp is at least one character long and has the 'L' format # which is not recognized for ASCII tables msg = ( "Column disp option (TDISPn) may not use the 'L' format " "with ASCII table columns. The invalid value will be " "ignored for the purpose of formatting the data in this " "column.") if msg is None: valid['disp'] = disp else: invalid['disp'] = (disp, msg) # Validate the start option if start is not None and start != '': msg = None if not isinstance(format, _AsciiColumnFormat): # The 'start' option only applies to ASCII columns msg = ( 'Column start option (TBCOLn) is not allowed for binary ' 'table columns (got {!r}). The invalid keyword will be ' 'ignored for the purpose of formatting the data in this ' 'column.'.format(start)) else: try: start = int(start) except (TypeError, ValueError): pass if not _is_int(start) or start < 1: msg = ( 'Column start option (TBCOLn) must be a positive integer ' '(got {!r}). The invalid value will be ignored for the ' 'purpose of formatting the data in this column.'.format(start)) if msg is None: valid['start'] = start else: invalid['start'] = (start, msg) # Process TDIMn options # ASCII table columns can't have a TDIMn keyword associated with it; # for now we just issue a warning and ignore it. # TODO: This should be checked by the FITS verification code if dim is not None and dim != '': msg = None dims_tuple = tuple() # NOTE: If valid, the dim keyword's value in the the valid dict is # a tuple, not the original string; if invalid just the original # string is returned if isinstance(format, _AsciiColumnFormat): msg = ( 'Column dim option (TDIMn) is not allowed for ASCII table ' 'columns (got {!r}). The invalid keyword will be ignored ' 'for the purpose of formatting this column.'.format(dim)) elif isinstance(dim, str): dims_tuple = _parse_tdim(dim) elif isinstance(dim, tuple): dims_tuple = dim else: msg = ( "`dim` argument must be a string containing a valid value " "for the TDIMn header keyword associated with this column, " "or a tuple containing the C-order dimensions for the " "column. The invalid value will be ignored for the purpose " "of formatting this column.") if dims_tuple: if reduce(operator.mul, dims_tuple) > format.repeat: msg = ( "The repeat count of the column format {!r} for column {!r} " "is fewer than the number of elements per the TDIM " "argument {!r}. The invalid TDIMn value will be ignored " "for the purpose of formatting this column.".format( name, format, dim)) if msg is None: valid['dim'] = dims_tuple else: invalid['dim'] = (dim, msg) if coord_type is not None and coord_type != '': msg = None if not isinstance(coord_type, str): msg = ( "Coordinate/axis type option (TCTYPn) must be a string " "(got {!r}). The invalid keyword will be ignored for the " "purpose of formatting this column.".format(coord_type)) elif len(coord_type) > 8: msg = ( "Coordinate/axis type option (TCTYPn) must be a string " "of atmost 8 characters (got {!r}). The invalid keyword " "will be ignored for the purpose of formatting this " "column.".format(coord_type)) if msg is None: valid['coord_type'] = coord_type else: invalid['coord_type'] = (coord_type, msg) if coord_unit is not None and coord_unit != '': msg = None if not isinstance(coord_unit, str): msg = ( "Coordinate/axis unit option (TCUNIn) must be a string " "(got {!r}). The invalid keyword will be ignored for the " "purpose of formatting this column.".format(coord_unit)) if msg is None: valid['coord_unit'] = coord_unit else: invalid['coord_unit'] = (coord_unit, msg) for k, v in [('coord_ref_point', coord_ref_point), ('coord_ref_value', coord_ref_value), ('coord_inc', coord_inc)]: if v is not None and v != '': msg = None if not isinstance(v, numbers.Real): msg = ( "Column {} option ({}n) must be a real floating type (got {!r}). " "The invalid value will be ignored for the purpose of formatting " "the data in this column.".format(k, ATTRIBUTE_TO_KEYWORD[k], v)) if msg is None: valid[k] = v else: invalid[k] = (v, msg) if time_ref_pos is not None and time_ref_pos != '': msg=None if not isinstance(time_ref_pos, str): msg = ( "Time coordinate reference position option (TRPOSn) must be " "a string (got {!r}). The invalid keyword will be ignored for " "the purpose of formatting this column.".format(time_ref_pos)) if msg is None: valid['time_ref_pos'] = time_ref_pos else: invalid['time_ref_pos'] = (time_ref_pos, msg) return valid, invalid @classmethod def _determine_formats(cls, format, start, dim, ascii): """ Given a format string and whether or not the Column is for an ASCII table (ascii=None means unspecified, but lean toward binary table where ambiguous) create an appropriate _BaseColumnFormat instance for the column's format, and determine the appropriate recarray format. The values of the start and dim keyword arguments are also useful, as the former is only valid for ASCII tables and the latter only for BINARY tables. """ # If the given format string is unambiguously a Numpy dtype or one of # the Numpy record format type specifiers supported by Astropy then that # should take priority--otherwise assume it is a FITS format if isinstance(format, np.dtype): format, _, _ = _dtype_to_recformat(format) # check format if ascii is None and not isinstance(format, _BaseColumnFormat): # We're just give a string which could be either a Numpy format # code, or a format for a binary column array *or* a format for an # ASCII column array--there may be many ambiguities here. Try our # best to guess what the user intended. format, recformat = cls._guess_format(format, start, dim) elif not ascii and not isinstance(format, _BaseColumnFormat): format, recformat = cls._convert_format(format, _ColumnFormat) elif ascii and not isinstance(format, _AsciiColumnFormat): format, recformat = cls._convert_format(format, _AsciiColumnFormat) else: # The format is already acceptable and unambiguous recformat = format.recformat return format, recformat @classmethod def _guess_format(cls, format, start, dim): if start and dim: # This is impossible; this can't be a valid FITS column raise ValueError( 'Columns cannot have both a start (TCOLn) and dim ' '(TDIMn) option, since the former is only applies to ' 'ASCII tables, and the latter is only valid for binary ' 'tables.') elif start: # Only ASCII table columns can have a 'start' option guess_format = _AsciiColumnFormat elif dim: # Only binary tables can have a dim option guess_format = _ColumnFormat else: # If the format is *technically* a valid binary column format # (i.e. it has a valid format code followed by arbitrary # "optional" codes), but it is also strictly a valid ASCII # table format, then assume an ASCII table column was being # requested (the more likely case, after all). with suppress(VerifyError): format = _AsciiColumnFormat(format, strict=True) # A safe guess which reflects the existing behavior of previous # Astropy versions guess_format = _ColumnFormat try: format, recformat = cls._convert_format(format, guess_format) except VerifyError: # For whatever reason our guess was wrong (for example if we got # just 'F' that's not a valid binary format, but it an ASCII format # code albeit with the width/precision omitted guess_format = (_AsciiColumnFormat if guess_format is _ColumnFormat else _ColumnFormat) # If this fails too we're out of options--it is truly an invalid # format, or at least not supported format, recformat = cls._convert_format(format, guess_format) return format, recformat def _convert_to_valid_data_type(self, array): # Convert the format to a type we understand if isinstance(array, Delayed): return array elif array is None: return array else: format = self.format dims = self._dims if dims: shape = dims[:-1] if 'A' in format else dims shape = (len(array),) + shape array = array.reshape(shape) if 'P' in format or 'Q' in format: return array elif 'A' in format: if array.dtype.char in 'SU': if dims: # The 'last' dimension (first in the order given # in the TDIMn keyword itself) is the number of # characters in each string fsize = dims[-1] else: fsize = np.dtype(format.recformat).itemsize return chararray.array(array, itemsize=fsize, copy=False) else: return _convert_array(array, np.dtype(format.recformat)) elif 'L' in format: # boolean needs to be scaled back to storage values ('T', 'F') if array.dtype == np.dtype('bool'): return np.where(array == np.False_, ord('F'), ord('T')) else: return np.where(array == 0, ord('F'), ord('T')) elif 'X' in format: return _convert_array(array, np.dtype('uint8')) else: # Preserve byte order of the original array for now; see #77 numpy_format = array.dtype.byteorder + format.recformat # Handle arrays passed in as unsigned ints as pseudo-unsigned # int arrays; blatantly tacked in here for now--we need columns # to have explicit knowledge of whether they treated as # pseudo-unsigned bzeros = {2: np.uint16(2**15), 4: np.uint32(2**31), 8: np.uint64(2**63)} if (array.dtype.kind == 'u' and array.dtype.itemsize in bzeros and self.bscale in (1, None, '') and self.bzero == bzeros[array.dtype.itemsize]): # Basically the array is uint, has scale == 1.0, and the # bzero is the appropriate value for a pseudo-unsigned # integer of the input dtype, then go ahead and assume that # uint is assumed numpy_format = numpy_format.replace('i', 'u') self._pseudo_unsigned_ints = True # The .base here means we're dropping the shape information, # which is only used to format recarray fields, and is not # useful for converting input arrays to the correct data type dtype = np.dtype(numpy_format).base return _convert_array(array, dtype)
[docs]class ColDefs(NotifierMixin): """ Column definitions class. It has attributes corresponding to the `Column` attributes (e.g. `ColDefs` has the attribute ``names`` while `Column` has ``name``). Each attribute in `ColDefs` is a list of corresponding attribute values from all `Column` objects. """ _padding_byte = '\x00' _col_format_cls = _ColumnFormat def __new__(cls, input, ascii=False): klass = cls if (hasattr(input, '_columns_type') and issubclass(input._columns_type, ColDefs)): klass = input._columns_type elif (hasattr(input, '_col_format_cls') and issubclass(input._col_format_cls, _AsciiColumnFormat)): klass = _AsciiColDefs if ascii: # force ASCII if this has been explicitly requested klass = _AsciiColDefs return object.__new__(klass) def __getnewargs__(self): return (self._arrays,) def __init__(self, input, ascii=False): """ Parameters ---------- input : sequence of `Column`, `ColDefs`, other An existing table HDU, an existing `ColDefs`, or any multi-field Numpy array or `numpy.recarray`. ascii : bool Use True to ensure that ASCII table columns are used. """ from .hdu.table import _TableBaseHDU from .fitsrec import FITS_rec if isinstance(input, ColDefs): self._init_from_coldefs(input) elif (isinstance(input, FITS_rec) and hasattr(input, '_coldefs') and input._coldefs): # If given a FITS_rec object we can directly copy its columns, but # only if its columns have already been defined, otherwise this # will loop back in on itself and blow up self._init_from_coldefs(input._coldefs) elif isinstance(input, np.ndarray) and input.dtype.fields is not None: # Construct columns from the fields of a record array self._init_from_array(input) elif isiterable(input): # if the input is a list of Columns self._init_from_sequence(input) elif isinstance(input, _TableBaseHDU): # Construct columns from fields in an HDU header self._init_from_table(input) else: raise TypeError('Input to ColDefs must be a table HDU, a list ' 'of Columns, or a record/field array.') # Listen for changes on all columns for col in self.columns: col._add_listener(self) def _init_from_coldefs(self, coldefs): """Initialize from an existing ColDefs object (just copy the columns and convert their formats if necessary). """ self.columns = [self._copy_column(col) for col in coldefs] def _init_from_sequence(self, columns): for idx, col in enumerate(columns): if not isinstance(col, Column): raise TypeError('Element {} in the ColDefs input is not a ' 'Column.'.format(idx)) self._init_from_coldefs(columns) def _init_from_array(self, array): self.columns = [] for idx in range(len(array.dtype)): cname = array.dtype.names[idx] ftype = array.dtype.fields[cname][0] format = self._col_format_cls.from_recformat(ftype) # Determine the appropriate dimensions for items in the column # (typically just 1D) dim = array.dtype[idx].shape[::-1] if dim and (len(dim) > 1 or 'A' in format): if 'A' in format: # n x m string arrays must include the max string # length in their dimensions (e.g. l x n x m) dim = (array.dtype[idx].base.itemsize,) + dim dim = repr(dim).replace(' ', '') else: dim = None # Check for unsigned ints. bzero = None if ftype.base.kind == 'u': if 'I' in format: bzero = np.uint16(2**15) elif 'J' in format: bzero = np.uint32(2**31) elif 'K' in format: bzero = np.uint64(2**63) c = Column(name=cname, format=format, array=array.view(np.ndarray)[cname], bzero=bzero, dim=dim) self.columns.append(c) def _init_from_table(self, table): hdr = table._header nfields = hdr['TFIELDS'] # go through header keywords to pick out column definition keywords # definition dictionaries for each field col_keywords = [{} for i in range(nfields)] for keyword, value in hdr.items(): key = TDEF_RE.match(keyword) try: keyword = key.group('label') except Exception: continue # skip if there is no match if keyword in KEYWORD_NAMES: col = int(key.group('num')) if 0 < col <= nfields: attr = KEYWORD_TO_ATTRIBUTE[keyword] if attr == 'format': # Go ahead and convert the format value to the # appropriate ColumnFormat container now value = self._col_format_cls(value) col_keywords[col - 1][attr] = value # Verify the column keywords and display any warnings if necessary; # we only want to pass on the valid keywords for idx, kwargs in enumerate(col_keywords): valid_kwargs, invalid_kwargs = Column._verify_keywords(**kwargs) for val in invalid_kwargs.values(): warnings.warn( 'Invalid keyword for column {}: {}'.format(idx + 1, val[1]), VerifyWarning) # Special cases for recformat and dim # TODO: Try to eliminate the need for these special cases del valid_kwargs['recformat'] if 'dim' in valid_kwargs: valid_kwargs['dim'] = kwargs['dim'] col_keywords[idx] = valid_kwargs # data reading will be delayed for col in range(nfields): col_keywords[col]['array'] = Delayed(table, col) # now build the columns self.columns = [Column(**attrs) for attrs in col_keywords] # Add the table HDU is a listener to changes to the columns # (either changes to individual columns, or changes to the set of # columns (add/remove/etc.)) self._add_listener(table) def __copy__(self): return self.__class__(self) def __deepcopy__(self, memo): return self.__class__([copy.deepcopy(c, memo) for c in self.columns]) def _copy_column(self, column): """Utility function used currently only by _init_from_coldefs to help convert columns from binary format to ASCII format or vice versa if necessary (otherwise performs a straight copy). """ if isinstance(column.format, self._col_format_cls): # This column has a FITS format compatible with this column # definitions class (that is ascii or binary) return column.copy() new_column = column.copy() # Try to use the Numpy recformat as the equivalency between the # two formats; if that conversion can't be made then these # columns can't be transferred # TODO: Catch exceptions here and raise an explicit error about # column format conversion new_column.format = self._col_format_cls.from_column_format( column.format) # Handle a few special cases of column format options that are not # compatible between ASCII an binary tables # TODO: This is sort of hacked in right now; we really need # separate classes for ASCII and Binary table Columns, and they # should handle formatting issues like these if not isinstance(new_column.format, _AsciiColumnFormat): # the column is a binary table column... new_column.start = None if new_column.null is not None: # We can't just "guess" a value to represent null # values in the new column, so just disable this for # now; users may modify it later new_column.null = None else: # the column is an ASCII table column... if new_column.null is not None: new_column.null = DEFAULT_ASCII_TNULL if (new_column.disp is not None and new_column.disp.upper().startswith('L')): # ASCII columns may not use the logical data display format; # for now just drop the TDISPn option for this column as we # don't have a systematic conversion of boolean data to ASCII # tables yet new_column.disp = None return new_column def __getattr__(self, name): """ Automatically returns the values for the given keyword attribute for all `Column`s in this list. Implements for example self.units, self.formats, etc. """ cname = name[:-1] if cname in KEYWORD_ATTRIBUTES and name[-1] == 's': attr = [] for col in self.columns: val = getattr(col, cname) attr.append(val if val is not None else '') return attr raise AttributeError(name) @lazyproperty def dtype(self): # Note: This previously returned a dtype that just used the raw field # widths based on the format's repeat count, and did not incorporate # field *shapes* as provided by TDIMn keywords. # Now this incorporates TDIMn from the start, which makes *this* method # a little more complicated, but simplifies code elsewhere (for example # fields will have the correct shapes even in the raw recarray). formats = [] offsets = [0] for format_, dim in zip(self.formats, self._dims): dt = format_.dtype if len(offsets) < len(self.formats): # Note: the size of the *original* format_ may be greater than # one would expect from the number of elements determined by # dim. The FITS format allows this--the rest of the field is # filled with undefined values. offsets.append(offsets[-1] + dt.itemsize) if dim: if format_.format == 'A': dt = np.dtype((dt.char + str(dim[-1]), dim[:-1])) else: dt = np.dtype((dt.base, dim)) formats.append(dt) return np.dtype({'names': self.names, 'formats': formats, 'offsets': offsets}) @lazyproperty def names(self): return [col.name for col in self.columns] @lazyproperty def formats(self): return [col.format for col in self.columns] @lazyproperty def _arrays(self): return [col.array for col in self.columns] @lazyproperty def _recformats(self): return [fmt.recformat for fmt in self.formats] @lazyproperty def _dims(self): """Returns the values of the TDIMn keywords parsed into tuples.""" return [col._dims for col in self.columns] def __getitem__(self, key): if isinstance(key, str): key = _get_index(self.names, key) x = self.columns[key] if _is_int(key): return x else: return ColDefs(x) def __len__(self): return len(self.columns) def __repr__(self): rep = 'ColDefs(' if hasattr(self, 'columns') and self.columns: # The hasattr check is mostly just useful in debugging sessions # where self.columns may not be defined yet rep += '\n ' rep += '\n '.join([repr(c) for c in self.columns]) rep += '\n' rep += ')' return rep def __add__(self, other, option='left'): if isinstance(other, Column): b = [other] elif isinstance(other, ColDefs): b = list(other.columns) else: raise TypeError('Wrong type of input.') if option == 'left': tmp = list(self.columns) + b else: tmp = b + list(self.columns) return ColDefs(tmp) def __radd__(self, other): return self.__add__(other, 'right') def __sub__(self, other): if not isinstance(other, (list, tuple)): other = [other] _other = [_get_index(self.names, key) for key in other] indx = list(range(len(self))) for x in _other: indx.remove(x) tmp = [self[i] for i in indx] return ColDefs(tmp) def _update_column_attribute_changed(self, column, attr, old_value, new_value): """ Handle column attribute changed notifications from columns that are members of this `ColDefs`. `ColDefs` itself does not currently do anything with this, and just bubbles the notification up to any listening table HDUs that may need to update their headers, etc. However, this also informs the table of the numerical index of the column that changed. """ idx = 0 for idx, col in enumerate(self.columns): if col is column: break if attr == 'name': del self.names elif attr == 'format': del self.formats self._notify('column_attribute_changed', column, idx, attr, old_value, new_value)
[docs] def add_col(self, column): """ Append one `Column` to the column definition. """ if not isinstance(column, Column): raise AssertionError self._arrays.append(column.array) # Obliterate caches of certain things del self.dtype del self._recformats del self._dims del self.names del self.formats self.columns.append(column) # Listen for changes on the new column column._add_listener(self) # If this ColDefs is being tracked by a Table, inform the # table that its data is now invalid. self._notify('column_added', self, column) return self
[docs] def del_col(self, col_name): """ Delete (the definition of) one `Column`. col_name : str or int The column's name or index """ indx = _get_index(self.names, col_name) col = self.columns[indx] del self._arrays[indx] # Obliterate caches of certain things del self.dtype del self._recformats del self._dims del self.names del self.formats del self.columns[indx] col._remove_listener(self) # If this ColDefs is being tracked by a table HDU, inform the HDU (or # any other listeners) that the column has been removed # Just send a reference to self, and the index of the column that was # removed self._notify('column_removed', self, indx) return self
[docs] def change_attrib(self, col_name, attrib, new_value): """ Change an attribute (in the ``KEYWORD_ATTRIBUTES`` list) of a `Column`. Parameters ---------- col_name : str or int The column name or index to change attrib : str The attribute name new_value : object The new value for the attribute """ setattr(self[col_name], attrib, new_value)
[docs] def change_name(self, col_name, new_name): """ Change a `Column`'s name. Parameters ---------- col_name : str The current name of the column new_name : str The new name of the column """ if new_name != col_name and new_name in self.names: raise ValueError(f'New name {new_name} already exists.') else: self.change_attrib(col_name, 'name', new_name)
[docs] def change_unit(self, col_name, new_unit): """ Change a `Column`'s unit. Parameters ---------- col_name : str or int The column name or index new_unit : str The new unit for the column """ self.change_attrib(col_name, 'unit', new_unit)
[docs] def info(self, attrib='all', output=None): """ Get attribute(s) information of the column definition. Parameters ---------- attrib : str Can be one or more of the attributes listed in ``astropy.io.fits.column.KEYWORD_ATTRIBUTES``. The default is ``"all"`` which will print out all attributes. It forgives plurals and blanks. If there are two or more attribute names, they must be separated by comma(s). output : file, optional File-like object to output to. Outputs to stdout by default. If `False`, returns the attributes as a `dict` instead. Notes ----- This function doesn't return anything by default; it just prints to stdout. """ if output is None: output = sys.stdout if attrib.strip().lower() in ['all', '']: lst = KEYWORD_ATTRIBUTES else: lst = attrib.split(',') for idx in range(len(lst)): lst[idx] = lst[idx].strip().lower() if lst[idx][-1] == 's': lst[idx] = list[idx][:-1] ret = {} for attr in lst: if output: if attr not in KEYWORD_ATTRIBUTES: output.write("'{}' is not an attribute of the column " "definitions.\n".format(attr)) continue output.write(f"{attr}:\n") output.write(' {}\n'.format(getattr(self, attr + 's'))) else: ret[attr] = getattr(self, attr + 's') if not output: return ret
class _AsciiColDefs(ColDefs): """ColDefs implementation for ASCII tables.""" _padding_byte = ' ' _col_format_cls = _AsciiColumnFormat def __init__(self, input, ascii=True): super().__init__(input) # if the format of an ASCII column has no width, add one if not isinstance(input, _AsciiColDefs): self._update_field_metrics() else: for idx, s in enumerate(input.starts): self.columns[idx].start = s self._spans = input.spans self._width = input._width @lazyproperty def dtype(self): dtype = {} for j in range(len(self)): data_type = 'S' + str(self.spans[j]) dtype[self.names[j]] = (data_type, self.starts[j] - 1) return np.dtype(dtype) @property def spans(self): """A list of the widths of each field in the table.""" return self._spans @lazyproperty def _recformats(self): if len(self) == 1: widths = [] else: widths = [y - x for x, y in pairwise(self.starts)] # Widths is the width of each field *including* any space between # fields; this is so that we can map the fields to string records in a # Numpy recarray widths.append(self._width - self.starts[-1] + 1) return ['a' + str(w) for w in widths] def add_col(self, column): super().add_col(column) self._update_field_metrics() def del_col(self, col_name): super().del_col(col_name) self._update_field_metrics() def _update_field_metrics(self): """ Updates the list of the start columns, the list of the widths of each field, and the total width of each record in the table. """ spans = [0] * len(self.columns) end_col = 0 # Refers to the ASCII text column, not the table col for idx, col in enumerate(self.columns): width = col.format.width # Update the start columns and column span widths taking into # account the case that the starting column of a field may not # be the column immediately after the previous field if not col.start: col.start = end_col + 1 end_col = col.start + width - 1 spans[idx] = width self._spans = spans self._width = end_col # Utilities class _VLF(np.ndarray): """Variable length field object.""" def __new__(cls, input, dtype='a'): """ Parameters ---------- input a sequence of variable-sized elements. """ if dtype == 'a': try: # this handles ['abc'] and [['a','b','c']] # equally, beautiful! input = [chararray.array(x, itemsize=1) for x in input] except Exception: raise ValueError( f'Inconsistent input data array: {input}') a = np.array(input, dtype=object) self = np.ndarray.__new__(cls, shape=(len(input),), buffer=a, dtype=object) self.max = 0 self.element_dtype = dtype return self def __array_finalize__(self, obj): if obj is None: return self.max = obj.max self.element_dtype = obj.element_dtype def __setitem__(self, key, value): """ To make sure the new item has consistent data type to avoid misalignment. """ if isinstance(value, np.ndarray) and value.dtype == self.dtype: pass elif isinstance(value, chararray.chararray) and value.itemsize == 1: pass elif self.element_dtype == 'a': value = chararray.array(value, itemsize=1) else: value = np.array(value, dtype=self.element_dtype) np.ndarray.__setitem__(self, key, value) self.max = max(self.max, len(value)) def _get_index(names, key): """ Get the index of the ``key`` in the ``names`` list. The ``key`` can be an integer or string. If integer, it is the index in the list. If string, a. Field (column) names are case sensitive: you can have two different columns called 'abc' and 'ABC' respectively. b. When you *refer* to a field (presumably with the field method), it will try to match the exact name first, so in the example in (a), field('abc') will get the first field, and field('ABC') will get the second field. If there is no exact name matched, it will try to match the name with case insensitivity. So, in the last example, field('Abc') will cause an exception since there is no unique mapping. If there is a field named "XYZ" and no other field name is a case variant of "XYZ", then field('xyz'), field('Xyz'), etc. will get this field. """ if _is_int(key): indx = int(key) elif isinstance(key, str): # try to find exact match first try: indx = names.index(key.rstrip()) except ValueError: # try to match case-insentively, _key = key.lower().rstrip() names = [n.lower().rstrip() for n in names] count = names.count(_key) # occurrence of _key in names if count == 1: indx = names.index(_key) elif count == 0: raise KeyError(f"Key '{key}' does not exist.") else: # multiple match raise KeyError(f"Ambiguous key name '{key}'.") else: raise KeyError(f"Illegal key '{key!r}'.") return indx def _unwrapx(input, output, repeat): """ Unwrap the X format column into a Boolean array. Parameters ---------- input input ``Uint8`` array of shape (`s`, `nbytes`) output output Boolean array of shape (`s`, `repeat`) repeat number of bits """ pow2 = np.array([128, 64, 32, 16, 8, 4, 2, 1], dtype='uint8') nbytes = ((repeat - 1) // 8) + 1 for i in range(nbytes): _min = i * 8 _max = min((i + 1) * 8, repeat) for j in range(_min, _max): output[..., j] = np.bitwise_and(input[..., i], pow2[j - i * 8]) def _wrapx(input, output, repeat): """ Wrap the X format column Boolean array into an ``UInt8`` array. Parameters ---------- input input Boolean array of shape (`s`, `repeat`) output output ``Uint8`` array of shape (`s`, `nbytes`) repeat number of bits """ output[...] = 0 # reset the output nbytes = ((repeat - 1) // 8) + 1 unused = nbytes * 8 - repeat for i in range(nbytes): _min = i * 8 _max = min((i + 1) * 8, repeat) for j in range(_min, _max): if j != _min: np.left_shift(output[..., i], 1, output[..., i]) np.add(output[..., i], input[..., j], output[..., i]) # shift the unused bits np.left_shift(output[..., i], unused, output[..., i]) def _makep(array, descr_output, format, nrows=None): """ Construct the P (or Q) format column array, both the data descriptors and the data. It returns the output "data" array of data type `dtype`. The descriptor location will have a zero offset for all columns after this call. The final offset will be calculated when the file is written. Parameters ---------- array input object array descr_output output "descriptor" array of data type int32 (for P format arrays) or int64 (for Q format arrays)--must be nrows long in its first dimension format the _FormatP object representing the format of the variable array nrows : int, optional number of rows to create in the column; defaults to the number of rows in the input array """ # TODO: A great deal of this is redundant with FITS_rec._convert_p; see if # we can merge the two somehow. _offset = 0 if not nrows: nrows = len(array) data_output = _VLF([None] * nrows, dtype=format.dtype) if format.dtype == 'a': _nbytes = 1 else: _nbytes = np.array([], dtype=format.dtype).itemsize for idx in range(nrows): if idx < len(array): rowval = array[idx] else: if format.dtype == 'a': rowval = ' ' * data_output.max else: rowval = [0] * data_output.max if format.dtype == 'a': data_output[idx] = chararray.array(encode_ascii(rowval), itemsize=1) else: data_output[idx] = np.array(rowval, dtype=format.dtype) descr_output[idx, 0] = len(data_output[idx]) descr_output[idx, 1] = _offset _offset += len(data_output[idx]) * _nbytes return data_output def _parse_tformat(tform): """Parse ``TFORMn`` keyword for a binary table into a ``(repeat, format, option)`` tuple. """ try: (repeat, format, option) = TFORMAT_RE.match(tform.strip()).groups() except Exception: # TODO: Maybe catch this error use a default type (bytes, maybe?) for # unrecognized column types. As long as we can determine the correct # byte width somehow.. raise VerifyError(f'Format {tform!r} is not recognized.') if repeat == '': repeat = 1 else: repeat = int(repeat) return (repeat, format.upper(), option) def _parse_ascii_tformat(tform, strict=False): """ Parse the ``TFORMn`` keywords for ASCII tables into a ``(format, width, precision)`` tuple (the latter is always zero unless format is one of 'E', 'F', or 'D'). """ match = TFORMAT_ASCII_RE.match(tform.strip()) if not match: raise VerifyError(f'Format {tform!r} is not recognized.') # Be flexible on case format = match.group('format') if format is None: # Floating point format format = match.group('formatf').upper() width = match.group('widthf') precision = match.group('precision') if width is None or precision is None: if strict: raise VerifyError('Format {!r} is not unambiguously an ASCII ' 'table format.') else: width = 0 if width is None else width precision = 1 if precision is None else precision else: format = format.upper() width = match.group('width') if width is None: if strict: raise VerifyError('Format {!r} is not unambiguously an ASCII ' 'table format.') else: # Just use a default width of 0 if unspecified width = 0 precision = 0 def convert_int(val): msg = ('Format {!r} is not valid--field width and decimal precision ' 'must be integers.') try: val = int(val) except (ValueError, TypeError): raise VerifyError(msg.format(tform)) return val if width and precision: # This should only be the case for floating-point formats width, precision = convert_int(width), convert_int(precision) elif width: # Just for integer/string formats; ignore precision width = convert_int(width) else: # For any format, if width was unspecified use the set defaults width, precision = ASCII_DEFAULT_WIDTHS[format] if width <= 0: raise VerifyError("Format {!r} not valid--field width must be a " "positive integeter.".format(tform)) if precision >= width: raise VerifyError("Format {!r} not valid--the number of decimal digits " "must be less than the format's total " "width {}.".format(tform, width)) return format, width, precision def _parse_tdim(tdim): """Parse the ``TDIM`` value into a tuple (may return an empty tuple if the value ``TDIM`` value is empty or invalid). """ m = tdim and TDIM_RE.match(tdim) if m: dims = m.group('dims') return tuple(int(d.strip()) for d in dims.split(','))[::-1] # Ignore any dim values that don't specify a multidimensional column return tuple() def _scalar_to_format(value): """ Given a scalar value or string, returns the minimum FITS column format that can represent that value. 'minimum' is defined by the order given in FORMATORDER. """ # First, if value is a string, try to convert to the appropriate scalar # value for type_ in (int, float, complex): try: value = type_(value) break except ValueError: continue numpy_dtype_str = np.min_scalar_type(value).str numpy_dtype_str = numpy_dtype_str[1:] # Strip endianness try: fits_format = NUMPY2FITS[numpy_dtype_str] return FITSUPCONVERTERS.get(fits_format, fits_format) except KeyError: return "A" + str(len(value)) def _cmp_recformats(f1, f2): """ Compares two numpy recformats using the ordering given by FORMATORDER. """ if f1[0] == 'a' and f2[0] == 'a': return cmp(int(f1[1:]), int(f2[1:])) else: f1, f2 = NUMPY2FITS[f1], NUMPY2FITS[f2] return cmp(FORMATORDER.index(f1), FORMATORDER.index(f2)) def _convert_fits2record(format): """ Convert FITS format spec to record format spec. """ repeat, dtype, option = _parse_tformat(format) if dtype in FITS2NUMPY: if dtype == 'A': output_format = FITS2NUMPY[dtype] + str(repeat) # to accommodate both the ASCII table and binary table column # format spec, i.e. A7 in ASCII table is the same as 7A in # binary table, so both will produce 'a7'. # Technically the FITS standard does not allow this but it's a very # common mistake if format.lstrip()[0] == 'A' and option != '': # make sure option is integer output_format = FITS2NUMPY[dtype] + str(int(option)) else: repeat_str = '' if repeat != 1: repeat_str = str(repeat) output_format = repeat_str + FITS2NUMPY[dtype] elif dtype == 'X': output_format = _FormatX(repeat) elif dtype == 'P': output_format = _FormatP.from_tform(format) elif dtype == 'Q': output_format = _FormatQ.from_tform(format) elif dtype == 'F': output_format = 'f8' else: raise ValueError(f'Illegal format `{format}`.') return output_format def _convert_record2fits(format): """ Convert record format spec to FITS format spec. """ recformat, kind, dtype = _dtype_to_recformat(format) shape = dtype.shape itemsize = dtype.base.itemsize if dtype.char == 'U': # Unicode dtype--itemsize is 4 times actual ASCII character length, # which what matters for FITS column formats # Use dtype.base--dtype may be a multi-dimensional dtype itemsize = itemsize // 4 option = str(itemsize) ndims = len(shape) repeat = 1 if ndims > 0: nel = np.array(shape, dtype='i8').prod() if nel > 1: repeat = nel if kind == 'a': # This is a kludge that will place string arrays into a # single field, so at least we won't lose data. Need to # use a TDIM keyword to fix this, declaring as (slength, # dim1, dim2, ...) as mwrfits does ntot = int(repeat) * int(option) output_format = str(ntot) + 'A' elif recformat in NUMPY2FITS: # record format if repeat != 1: repeat = str(repeat) else: repeat = '' output_format = repeat + NUMPY2FITS[recformat] else: raise ValueError(f'Illegal format `{format}`.') return output_format def _dtype_to_recformat(dtype): """ Utility function for converting a dtype object or string that instantiates a dtype (e.g. 'float32') into one of the two character Numpy format codes that have been traditionally used by Astropy. In particular, use of 'a' to refer to character data is long since deprecated in Numpy, but Astropy remains heavily invested in its use (something to try to get away from sooner rather than later). """ if not isinstance(dtype, np.dtype): dtype = np.dtype(dtype) kind = dtype.base.kind if kind in ('U', 'S'): recformat = kind = 'a' else: itemsize = dtype.base.itemsize recformat = kind + str(itemsize) return recformat, kind, dtype def _convert_format(format, reverse=False): """ Convert FITS format spec to record format spec. Do the opposite if reverse=True. """ if reverse: return _convert_record2fits(format) else: return _convert_fits2record(format) def _convert_ascii_format(format, reverse=False): """Convert ASCII table format spec to record format spec.""" if reverse: recformat, kind, dtype = _dtype_to_recformat(format) itemsize = dtype.itemsize if kind == 'a': return 'A' + str(itemsize) elif NUMPY2FITS.get(recformat) == 'L': # Special case for logical/boolean types--for ASCII tables we # represent these as single character columns containing 'T' or 'F' # (a la the storage format for Logical columns in binary tables) return 'A1' elif kind == 'i': # Use for the width the maximum required to represent integers # of that byte size plus 1 for signs, but use a minimum of the # default width (to keep with existing behavior) width = 1 + len(str(2 ** (itemsize * 8))) width = max(width, ASCII_DEFAULT_WIDTHS['I'][0]) return 'I' + str(width) elif kind == 'f': # This is tricky, but go ahead and use D if float-64, and E # if float-32 with their default widths if itemsize >= 8: format = 'D' else: format = 'E' width = '.'.join(str(w) for w in ASCII_DEFAULT_WIDTHS[format]) return format + width # TODO: There may be reasonable ways to represent other Numpy types so # let's see what other possibilities there are besides just 'a', 'i', # and 'f'. If it doesn't have a reasonable ASCII representation then # raise an exception else: format, width, precision = _parse_ascii_tformat(format) # This gives a sensible "default" dtype for a given ASCII # format code recformat = ASCII2NUMPY[format] # The following logic is taken from CFITSIO: # For integers, if the width <= 4 we can safely use 16-bit ints for all # values [for the non-standard J format code just always force 64-bit] if format == 'I' and width <= 4: recformat = 'i2' elif format == 'A': recformat += str(width) return recformat def _parse_tdisp_format(tdisp): """ Parse the ``TDISPn`` keywords for ASCII and binary tables into a ``(format, width, precision, exponential)`` tuple (the TDISP values for ASCII and binary are identical except for 'Lw', which is only present in BINTABLE extensions Parameters ---------- tdisp: str TDISPn FITS Header keyword. Used to specify display formatting. Returns ------- formatc: str The format characters from TDISPn width: str The width int value from TDISPn precision: str The precision int value from TDISPn exponential: str The exponential int value from TDISPn """ # Use appropriate regex for format type tdisp = tdisp.strip() fmt_key = tdisp[0] if tdisp[0] !='E' or tdisp[1] not in 'NS' else tdisp[:2] try: tdisp_re = TDISP_RE_DICT[fmt_key] except KeyError: raise VerifyError(f'Format {tdisp} is not recognized.') match = tdisp_re.match(tdisp.strip()) if not match or match.group('formatc') is None: raise VerifyError(f'Format {tdisp} is not recognized.') formatc = match.group('formatc') width = match.group('width') precision = None exponential = None # Some formats have precision and exponential if tdisp[0] in ('I', 'B', 'O', 'Z', 'F', 'E', 'G', 'D'): precision = match.group('precision') if precision is None: precision = 1 if tdisp[0] in ('E', 'D', 'G') and tdisp[1] not in ('N', 'S'): exponential = match.group('exponential') if exponential is None: exponential = 1 # Once parsed, check format dict to do conversion to a formatting string return formatc, width, precision, exponential def _fortran_to_python_format(tdisp): """ Turn the TDISPn fortran format pieces into a final Python format string. See the format_type definitions above the TDISP_FMT_DICT. If codes is changed to take advantage of the exponential specification, will need to add it as another input parameter. Parameters ---------- tdisp: str TDISPn FITS Header keyword. Used to specify display formatting. Returns ------- format_string: str The TDISPn keyword string translated into a Python format string. """ format_type, width, precision, exponential = _parse_tdisp_format(tdisp) try: fmt = TDISP_FMT_DICT[format_type] return fmt.format(width=width, precision=precision) except KeyError: raise VerifyError(f'Format {format_type} is not recognized.') def python_to_tdisp(format_string, logical_dtype = False): """ Turn the Python format string to a TDISP FITS compliant format string. Not all formats convert. these will cause a Warning and return None. Parameters ---------- format_string: str TDISPn FITS Header keyword. Used to specify display formatting. logical_dtype: bool True is this format type should be a logical type, 'L'. Needs special handeling. Returns ------- tdsip_string: str The TDISPn keyword string translated into a Python format string. """ fmt_to_tdisp = {'a': 'A', 's': 'A', 'd': 'I', 'b': 'B', 'o': 'O', 'x': 'Z', 'X': 'Z', 'f': 'F', 'F': 'F', 'g': 'G', 'G': 'G', 'e': 'E', 'E': 'E'} if format_string in [None, "", "{}"]: return None # Strip out extra format characters that aren't a type or a width/precision if format_string[0] == '{' and format_string != "{}": fmt_str = format_string.lstrip("{:").rstrip('}') elif format_string[0] == '%': fmt_str = format_string.lstrip("%") else: fmt_str = format_string precision, sep = '', '' # Character format, only translate right aligned, and don't take zero fills if fmt_str[-1].isdigit() and fmt_str[0] == '>' and fmt_str[1] != '0': ftype = fmt_to_tdisp['a'] width = fmt_str[1:] elif fmt_str[-1] == 's' and fmt_str != 's': ftype = fmt_to_tdisp['a'] width = fmt_str[:-1].lstrip('0') # Number formats, don't take zero fills elif fmt_str[-1].isalpha() and len(fmt_str) > 1 and fmt_str[0] != '0': ftype = fmt_to_tdisp[fmt_str[-1]] fmt_str = fmt_str[:-1] # If format has a "." split out the width and precision if '.' in fmt_str: width, precision = fmt_str.split('.') sep = '.' if width == "": ascii_key = ftype if ftype != 'G' else 'F' width = str(int(precision) + (ASCII_DEFAULT_WIDTHS[ascii_key][0] - ASCII_DEFAULT_WIDTHS[ascii_key][1])) # Otherwise we just have a width else: width = fmt_str else: warnings.warn('Format {} cannot be mapped to the accepted ' 'TDISPn keyword values. Format will not be ' 'moved into TDISPn keyword.'.format(format_string), AstropyUserWarning) return None # Catch logical data type, set the format type back to L in this case if logical_dtype: ftype = 'L' return ftype + width + sep + precision