Source code for astropy.io.fits.hdu.hdulist

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


import gzip
import itertools
import os
import shutil
import sys
import warnings

import numpy as np

from . import compressed
from .base import _BaseHDU, _ValidHDU, _NonstandardHDU, ExtensionHDU
from .groups import GroupsHDU
from .image import PrimaryHDU, ImageHDU
from astropy.io.fits.file import _File, FILE_MODES
from astropy.io.fits.header import _pad_length
from astropy.io.fits.util import (_free_space_check, _get_array_mmap, _is_int,
                                  _tmp_name, fileobj_closed, fileobj_mode,
                                  ignore_sigint, isfile)
from astropy.io.fits.verify import _Verify, _ErrList, VerifyError, VerifyWarning
from astropy.utils import indent
from astropy.utils.exceptions import AstropyUserWarning
from astropy.utils.decorators import deprecated_renamed_argument

try:
    import bz2
except ImportError:
    HAS_BZ2 = False
else:
    HAS_BZ2 = True


def fitsopen(name, mode='readonly', memmap=None, save_backup=False,
             cache=True, lazy_load_hdus=None, **kwargs):
    """Factory function to open a FITS file and return an `HDUList` object.

    Parameters
    ----------
    name : file path, file object, file-like object or pathlib.Path object
        File to be opened.

    mode : str, optional
        Open mode, 'readonly', 'update', 'append', 'denywrite', or
        'ostream'. Default is 'readonly'.

        If ``name`` is a file object that is already opened, ``mode`` must
        match the mode the file was opened with, readonly (rb), update (rb+),
        append (ab+), ostream (w), denywrite (rb)).

    memmap : bool, optional
        Is memory mapping to be used? This value is obtained from the
        configuration item ``astropy.io.fits.Conf.use_memmap``.
        Default is `True`.

    save_backup : bool, optional
        If the file was opened in update or append mode, this ensures that
        a backup of the original file is saved before any changes are flushed.
        The backup has the same name as the original file with ".bak" appended.
        If "file.bak" already exists then "file.bak.1" is used, and so on.
        Default is `False`.

    cache : bool, optional
        If the file name is a URL, `~astropy.utils.data.download_file` is used
        to open the file.  This specifies whether or not to save the file
        locally in Astropy's download cache. Default is `True`.

    lazy_load_hdus : bool, optional
        To avoid reading all the HDUs and headers in a FITS file immediately
        upon opening.  This is an optimization especially useful for large
        files, as FITS has no way of determining the number and offsets of all
        the HDUs in a file without scanning through the file and reading all
        the headers. Default is `True`.

        To disable lazy loading and read all HDUs immediately (the old
        behavior) use ``lazy_load_hdus=False``.  This can lead to fewer
        surprises--for example with lazy loading enabled, ``len(hdul)``
        can be slow, as it means the entire FITS file needs to be read in
        order to determine the number of HDUs.  ``lazy_load_hdus=False``
        ensures that all HDUs have already been loaded after the file has
        been opened.

        .. versionadded:: 1.3

    uint : bool, optional
        Interpret signed integer data where ``BZERO`` is the central value and
        ``BSCALE == 1`` as unsigned integer data.  For example, ``int16`` data
        with ``BZERO = 32768`` and ``BSCALE = 1`` would be treated as
        ``uint16`` data. Default is `True` so that the pseudo-unsigned
        integer convention is assumed.

    ignore_missing_end : bool, optional
        Do not issue an exception when opening a file that is missing an
        ``END`` card in the last header. Default is `False`.

    checksum : bool, str, optional
        If `True`, verifies that both ``DATASUM`` and ``CHECKSUM`` card values
        (when present in the HDU header) match the header and data of all HDU's
        in the file.  Updates to a file that already has a checksum will
        preserve and update the existing checksums unless this argument is
        given a value of 'remove', in which case the CHECKSUM and DATASUM
        values are not checked, and are removed when saving changes to the
        file. Default is `False`.

    disable_image_compression : bool, optional
        If `True`, treats compressed image HDU's like normal binary table
        HDU's.  Default is `False`.

    do_not_scale_image_data : bool, optional
        If `True`, image data is not scaled using BSCALE/BZERO values
        when read.  Default is `False`.

    character_as_bytes : bool, optional
        Whether to return bytes for string columns, otherwise unicode strings
        are returned, but this does not respect memory mapping and loads the
        whole column in memory when accessed. Default is `False`.

    ignore_blank : bool, optional
        If `True`, the BLANK keyword is ignored if present.
        Default is `False`.

    scale_back : bool, optional
        If `True`, when saving changes to a file that contained scaled image
        data, restore the data to the original type and reapply the original
        BSCALE/BZERO values. This could lead to loss of accuracy if scaling
        back to integer values after performing floating point operations on
        the data. Default is `False`.

    Returns
    -------
        hdulist : an `HDUList` object
            `HDUList` containing all of the header data units in the file.

    """

    from astropy.io.fits import conf

    if memmap is None:
        # distinguish between True (kwarg explicitly set)
        # and None (preference for memmap in config, might be ignored)
        memmap = None if conf.use_memmap else False
    else:
        memmap = bool(memmap)

    if lazy_load_hdus is None:
        lazy_load_hdus = conf.lazy_load_hdus
    else:
        lazy_load_hdus = bool(lazy_load_hdus)

    if 'uint' not in kwargs:
        kwargs['uint'] = conf.enable_uint

    if not name:
        raise ValueError(f'Empty filename: {name!r}')

    return HDUList.fromfile(name, mode, memmap, save_backup, cache,
                            lazy_load_hdus, **kwargs)


[docs]class HDUList(list, _Verify): """ HDU list class. This is the top-level FITS object. When a FITS file is opened, a `HDUList` object is returned. """ def __init__(self, hdus=[], file=None): """ Construct a `HDUList` object. Parameters ---------- hdus : sequence of HDU objects or single HDU, optional The HDU object(s) to comprise the `HDUList`. Should be instances of HDU classes like `ImageHDU` or `BinTableHDU`. file : file object, bytes, optional The opened physical file associated with the `HDUList` or a bytes object containing the contents of the FITS file. """ if isinstance(file, bytes): self._data = file self._file = None else: self._file = file self._data = None self._save_backup = False # For internal use only--the keyword args passed to fitsopen / # HDUList.fromfile/string when opening the file self._open_kwargs = {} self._in_read_next_hdu = False # If we have read all the HDUs from the file or not # The assumes that all HDUs have been written when we first opened the # file; we do not currently support loading additional HDUs from a file # while it is being streamed to. In the future that might be supported # but for now this is only used for the purpose of lazy-loading of # existing HDUs. if file is None: self._read_all = True elif self._file is not None: # Should never attempt to read HDUs in ostream mode self._read_all = self._file.mode == 'ostream' else: self._read_all = False if hdus is None: hdus = [] # can take one HDU, as well as a list of HDU's as input if isinstance(hdus, _ValidHDU): hdus = [hdus] elif not isinstance(hdus, (HDUList, list)): raise TypeError("Invalid input for HDUList.") for idx, hdu in enumerate(hdus): if not isinstance(hdu, _BaseHDU): raise TypeError("Element {} in the HDUList input is " "not an HDU.".format(idx)) super().__init__(hdus) if file is None: # Only do this when initializing from an existing list of HDUs # When initalizing from a file, this will be handled by the # append method after the first HDU is read self.update_extend() def __len__(self): if not self._in_read_next_hdu: self.readall() return super().__len__() def __repr__(self): # In order to correctly repr an HDUList we need to load all the # HDUs as well self.readall() return super().__repr__() def __iter__(self): # While effectively this does the same as: # for idx in range(len(self)): # yield self[idx] # the more complicated structure is here to prevent the use of len(), # which would break the lazy loading for idx in itertools.count(): try: yield self[idx] except IndexError: break def __getitem__(self, key): """ Get an HDU from the `HDUList`, indexed by number or name. """ # If the key is a slice we need to make sure the necessary HDUs # have been loaded before passing the slice on to super. if isinstance(key, slice): max_idx = key.stop # Check for and handle the case when no maximum was # specified (e.g. [1:]). if max_idx is None: # We need all of the HDUs, so load them # and reset the maximum to the actual length. max_idx = len(self) # Just in case the max_idx is negative... max_idx = self._positive_index_of(max_idx) number_loaded = super().__len__() if max_idx >= number_loaded: # We need more than we have, try loading up to and including # max_idx. Note we do not try to be clever about skipping HDUs # even though key.step might conceivably allow it. for i in range(number_loaded, max_idx): # Read until max_idx or to the end of the file, whichever # comes first. if not self._read_next_hdu(): break try: hdus = super().__getitem__(key) except IndexError as e: # Raise a more helpful IndexError if the file was not fully read. if self._read_all: raise e else: raise IndexError('HDU not found, possibly because the index ' 'is out of range, or because the file was ' 'closed before all HDUs were read') else: return HDUList(hdus) # Originally this used recursion, but hypothetically an HDU with # a very large number of HDUs could blow the stack, so use a loop # instead try: return self._try_while_unread_hdus(super().__getitem__, self._positive_index_of(key)) except IndexError as e: # Raise a more helpful IndexError if the file was not fully read. if self._read_all: raise e else: raise IndexError('HDU not found, possibly because the index ' 'is out of range, or because the file was ' 'closed before all HDUs were read') def __contains__(self, item): """ Returns `True` if ``item`` is an ``HDU`` _in_ ``self`` or a valid extension specification (e.g., integer extension number, extension name, or a tuple of extension name and an extension version) of a ``HDU`` in ``self``. """ try: self._try_while_unread_hdus(self.index_of, item) except (KeyError, ValueError): return False return True def __setitem__(self, key, hdu): """ Set an HDU to the `HDUList`, indexed by number or name. """ _key = self._positive_index_of(key) if isinstance(hdu, (slice, list)): if _is_int(_key): raise ValueError('An element in the HDUList must be an HDU.') for item in hdu: if not isinstance(item, _BaseHDU): raise ValueError(f'{item} is not an HDU.') else: if not isinstance(hdu, _BaseHDU): raise ValueError(f'{hdu} is not an HDU.') try: self._try_while_unread_hdus(super().__setitem__, _key, hdu) except IndexError: raise IndexError('Extension {} is out of bound or not found.' .format(key)) self._resize = True self._truncate = False def __delitem__(self, key): """ Delete an HDU from the `HDUList`, indexed by number or name. """ if isinstance(key, slice): end_index = len(self) else: key = self._positive_index_of(key) end_index = len(self) - 1 self._try_while_unread_hdus(super().__delitem__, key) if (key == end_index or key == -1 and not self._resize): self._truncate = True else: self._truncate = False self._resize = True # Support the 'with' statement def __enter__(self): return self def __exit__(self, type, value, traceback): self.close()
[docs] @classmethod def fromfile(cls, fileobj, mode=None, memmap=None, save_backup=False, cache=True, lazy_load_hdus=True, **kwargs): """ Creates an `HDUList` instance from a file-like object. The actual implementation of ``fitsopen()``, and generally shouldn't be used directly. Use :func:`open` instead (and see its documentation for details of the parameters accepted by this method). """ return cls._readfrom(fileobj=fileobj, mode=mode, memmap=memmap, save_backup=save_backup, cache=cache, lazy_load_hdus=lazy_load_hdus, **kwargs)
[docs] @classmethod def fromstring(cls, data, **kwargs): """ Creates an `HDUList` instance from a string or other in-memory data buffer containing an entire FITS file. Similar to :meth:`HDUList.fromfile`, but does not accept the mode or memmap arguments, as they are only relevant to reading from a file on disk. This is useful for interfacing with other libraries such as CFITSIO, and may also be useful for streaming applications. Parameters ---------- data : str, buffer, memoryview, etc. A string or other memory buffer containing an entire FITS file. It should be noted that if that memory is read-only (such as a Python string) the returned :class:`HDUList`'s data portions will also be read-only. kwargs : dict Optional keyword arguments. See :func:`astropy.io.fits.open` for details. Returns ------- hdul : HDUList An :class:`HDUList` object representing the in-memory FITS file. """ try: # Test that the given object supports the buffer interface by # ensuring an ndarray can be created from it np.ndarray((), dtype='ubyte', buffer=data) except TypeError: raise TypeError( 'The provided object {} does not contain an underlying ' 'memory buffer. fromstring() requires an object that ' 'supports the buffer interface such as bytes, buffer, ' 'memoryview, ndarray, etc. This restriction is to ensure ' 'that efficient access to the array/table data is possible.' ''.format(data)) return cls._readfrom(data=data, **kwargs)
[docs] def fileinfo(self, index): """ Returns a dictionary detailing information about the locations of the indexed HDU within any associated file. The values are only valid after a read or write of the associated file with no intervening changes to the `HDUList`. Parameters ---------- index : int Index of HDU for which info is to be returned. Returns ------- fileinfo : dict or None The dictionary details information about the locations of the indexed HDU within an associated file. Returns `None` when the HDU is not associated with a file. Dictionary contents: ========== ======================================================== Key Value ========== ======================================================== file File object associated with the HDU filename Name of associated file object filemode Mode in which the file was opened (readonly, update, append, denywrite, ostream) resized Flag that when `True` indicates that the data has been resized since the last read/write so the returned values may not be valid. hdrLoc Starting byte location of header in file datLoc Starting byte location of data block in file datSpan Data size including padding ========== ======================================================== """ if self._file is not None: output = self[index].fileinfo() if not output: # OK, the HDU associated with this index is not yet # tied to the file associated with the HDUList. The only way # to get the file object is to check each of the HDU's in the # list until we find the one associated with the file. f = None for hdu in self: info = hdu.fileinfo() if info: f = info['file'] fm = info['filemode'] break output = {'file': f, 'filemode': fm, 'hdrLoc': None, 'datLoc': None, 'datSpan': None} output['filename'] = self._file.name output['resized'] = self._wasresized() else: output = None return output
def __copy__(self): """ Return a shallow copy of an HDUList. Returns ------- copy : `HDUList` A shallow copy of this `HDUList` object. """ return self[:] # Syntactic sugar for `__copy__()` magic method copy = __copy__ def __deepcopy__(self, memo=None): return HDUList([hdu.copy() for hdu in self])
[docs] def pop(self, index=-1): """ Remove an item from the list and return it. Parameters ---------- index : int, str, tuple of (string, int), optional An integer value of ``index`` indicates the position from which ``pop()`` removes and returns an HDU. A string value or a tuple of ``(string, int)`` functions as a key for identifying the HDU to be removed and returned. If ``key`` is a tuple, it is of the form ``(key, ver)`` where ``ver`` is an ``EXTVER`` value that must match the HDU being searched for. If the key is ambiguous (e.g. there are multiple 'SCI' extensions) the first match is returned. For a more precise match use the ``(name, ver)`` pair. If even the ``(name, ver)`` pair is ambiguous the numeric index must be used to index the duplicate HDU. Returns ------- hdu : HDU object The HDU object at position indicated by ``index`` or having name and version specified by ``index``. """ # Make sure that HDUs are loaded before attempting to pop self.readall() list_index = self.index_of(index) return super().pop(list_index)
[docs] def insert(self, index, hdu): """ Insert an HDU into the `HDUList` at the given ``index``. Parameters ---------- index : int Index before which to insert the new HDU. hdu : HDU object The HDU object to insert """ if not isinstance(hdu, _BaseHDU): raise ValueError(f'{hdu} is not an HDU.') num_hdus = len(self) if index == 0 or num_hdus == 0: if num_hdus != 0: # We are inserting a new Primary HDU so we need to # make the current Primary HDU into an extension HDU. if isinstance(self[0], GroupsHDU): raise ValueError( "The current Primary HDU is a GroupsHDU. " "It can't be made into an extension HDU, " "so another HDU cannot be inserted before it.") hdu1 = ImageHDU(self[0].data, self[0].header) # Insert it into position 1, then delete HDU at position 0. super().insert(1, hdu1) super().__delitem__(0) if not isinstance(hdu, (PrimaryHDU, _NonstandardHDU)): # You passed in an Extension HDU but we need a Primary HDU. # If you provided an ImageHDU then we can convert it to # a primary HDU and use that. if isinstance(hdu, ImageHDU): hdu = PrimaryHDU(hdu.data, hdu.header) else: # You didn't provide an ImageHDU so we create a # simple Primary HDU and append that first before # we append the new Extension HDU. phdu = PrimaryHDU() super().insert(0, phdu) index = 1 else: if isinstance(hdu, GroupsHDU): raise ValueError('A GroupsHDU must be inserted as a ' 'Primary HDU.') if isinstance(hdu, PrimaryHDU): # You passed a Primary HDU but we need an Extension HDU # so create an Extension HDU from the input Primary HDU. hdu = ImageHDU(hdu.data, hdu.header) super().insert(index, hdu) hdu._new = True self._resize = True self._truncate = False # make sure the EXTEND keyword is in primary HDU if there is extension self.update_extend()
[docs] def append(self, hdu): """ Append a new HDU to the `HDUList`. Parameters ---------- hdu : HDU object HDU to add to the `HDUList`. """ if not isinstance(hdu, _BaseHDU): raise ValueError('HDUList can only append an HDU.') if len(self) > 0: if isinstance(hdu, GroupsHDU): raise ValueError( "Can't append a GroupsHDU to a non-empty HDUList") if isinstance(hdu, PrimaryHDU): # You passed a Primary HDU but we need an Extension HDU # so create an Extension HDU from the input Primary HDU. # TODO: This isn't necessarily sufficient to copy the HDU; # _header_offset and friends need to be copied too. hdu = ImageHDU(hdu.data, hdu.header) else: if not isinstance(hdu, (PrimaryHDU, _NonstandardHDU)): # You passed in an Extension HDU but we need a Primary # HDU. # If you provided an ImageHDU then we can convert it to # a primary HDU and use that. if isinstance(hdu, ImageHDU): hdu = PrimaryHDU(hdu.data, hdu.header) else: # You didn't provide an ImageHDU so we create a # simple Primary HDU and append that first before # we append the new Extension HDU. phdu = PrimaryHDU() super().append(phdu) super().append(hdu) hdu._new = True self._resize = True self._truncate = False # make sure the EXTEND keyword is in primary HDU if there is extension self.update_extend()
[docs] def index_of(self, key): """ Get the index of an HDU from the `HDUList`. Parameters ---------- key : int, str, tuple of (string, int) or an HDU object The key identifying the HDU. If ``key`` is a tuple, it is of the form ``(name, ver)`` where ``ver`` is an ``EXTVER`` value that must match the HDU being searched for. If the key is ambiguous (e.g. there are multiple 'SCI' extensions) the first match is returned. For a more precise match use the ``(name, ver)`` pair. If even the ``(name, ver)`` pair is ambiguous (it shouldn't be but it's not impossible) the numeric index must be used to index the duplicate HDU. When ``key`` is an HDU object, this function returns the index of that HDU object in the ``HDUList``. Returns ------- index : int The index of the HDU in the `HDUList`. Raises ------ ValueError If ``key`` is an HDU object and it is not found in the ``HDUList``. KeyError If an HDU specified by the ``key`` that is an extension number, extension name, or a tuple of extension name and version is not found in the ``HDUList``. """ if _is_int(key): return key elif isinstance(key, tuple): _key, _ver = key elif isinstance(key, _BaseHDU): return self.index(key) else: _key = key _ver = None if not isinstance(_key, str): raise KeyError( '{} indices must be integers, extension names as strings, ' 'or (extname, version) tuples; got {}' ''.format(self.__class__.__name__, _key)) _key = (_key.strip()).upper() found = None for idx, hdu in enumerate(self): name = hdu.name if isinstance(name, str): name = name.strip().upper() # 'PRIMARY' should always work as a reference to the first HDU if ((name == _key or (_key == 'PRIMARY' and idx == 0)) and (_ver is None or _ver == hdu.ver)): found = idx break if (found is None): raise KeyError(f'Extension {key!r} not found.') else: return found
def _positive_index_of(self, key): """ Same as index_of, but ensures always returning a positive index or zero. (Really this should be called non_negative_index_of but it felt too long.) This means that if the key is a negative integer, we have to convert it to the corresponding positive index. This means knowing the length of the HDUList, which in turn means loading all HDUs. Therefore using negative indices on HDULists is inherently inefficient. """ index = self.index_of(key) if index >= 0: return index if abs(index) > len(self): raise IndexError( f'Extension {index} is out of bound or not found.') return len(self) + index
[docs] def readall(self): """ Read data of all HDUs into memory. """ while self._read_next_hdu(): pass
[docs] @ignore_sigint def flush(self, output_verify='fix', verbose=False): """ Force a write of the `HDUList` back to the file (for append and update modes only). Parameters ---------- output_verify : str Output verification option. Must be one of ``"fix"``, ``"silentfix"``, ``"ignore"``, ``"warn"``, or ``"exception"``. May also be any combination of ``"fix"`` or ``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception" (e.g. ``"fix+warn"``). See :ref:`verify` for more info. verbose : bool When `True`, print verbose messages """ if self._file.mode not in ('append', 'update', 'ostream'): warnings.warn("Flush for '{}' mode is not supported." .format(self._file.mode), AstropyUserWarning) return if self._save_backup and self._file.mode in ('append', 'update'): filename = self._file.name if os.path.exists(filename): # The the file doesn't actually exist anymore for some reason # then there's no point in trying to make a backup backup = filename + '.bak' idx = 1 while os.path.exists(backup): backup = filename + '.bak.' + str(idx) idx += 1 warnings.warn('Saving a backup of {} to {}.'.format( filename, backup), AstropyUserWarning) try: shutil.copy(filename, backup) except OSError as exc: raise OSError('Failed to save backup to destination {}: ' '{}'.format(filename, exc)) self.verify(option=output_verify) if self._file.mode in ('append', 'ostream'): for hdu in self: if verbose: try: extver = str(hdu._header['extver']) except KeyError: extver = '' # only append HDU's which are "new" if hdu._new: hdu._prewriteto(checksum=hdu._output_checksum) with _free_space_check(self): hdu._writeto(self._file) if verbose: print('append HDU', hdu.name, extver) hdu._new = False hdu._postwriteto() elif self._file.mode == 'update': self._flush_update()
[docs] def update_extend(self): """ Make sure that if the primary header needs the keyword ``EXTEND`` that it has it and it is correct. """ if not len(self): return if not isinstance(self[0], PrimaryHDU): # A PrimaryHDU will be automatically inserted at some point, but it # might not have been added yet return hdr = self[0].header def get_first_ext(): try: return self[1] except IndexError: return None if 'EXTEND' in hdr: if not hdr['EXTEND'] and get_first_ext() is not None: hdr['EXTEND'] = True elif get_first_ext() is not None: if hdr['NAXIS'] == 0: hdr.set('EXTEND', True, after='NAXIS') else: n = hdr['NAXIS'] hdr.set('EXTEND', True, after='NAXIS' + str(n))
[docs] @deprecated_renamed_argument('clobber', 'overwrite', '2.0') def writeto(self, fileobj, output_verify='exception', overwrite=False, checksum=False): """ Write the `HDUList` to a new file. Parameters ---------- fileobj : file path, file object or file-like object File to write to. If a file object, must be opened in a writeable mode. output_verify : str Output verification option. Must be one of ``"fix"``, ``"silentfix"``, ``"ignore"``, ``"warn"``, or ``"exception"``. May also be any combination of ``"fix"`` or ``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception" (e.g. ``"fix+warn"``). See :ref:`verify` for more info. overwrite : bool, optional If ``True``, overwrite the output file if it exists. Raises an ``OSError`` if ``False`` and the output file exists. Default is ``False``. .. versionchanged:: 1.3 ``overwrite`` replaces the deprecated ``clobber`` argument. checksum : bool When `True` adds both ``DATASUM`` and ``CHECKSUM`` cards to the headers of all HDU's written to the file. """ if (len(self) == 0): warnings.warn("There is nothing to write.", AstropyUserWarning) return self.verify(option=output_verify) # make sure the EXTEND keyword is there if there is extension self.update_extend() # make note of whether the input file object is already open, in which # case we should not close it after writing (that should be the job # of the caller) closed = isinstance(fileobj, str) or fileobj_closed(fileobj) mode = FILE_MODES[fileobj_mode(fileobj)] if isfile(fileobj) else 'ostream' # This can accept an open file object that's open to write only, or in # append/update modes but only if the file doesn't exist. fileobj = _File(fileobj, mode=mode, overwrite=overwrite) hdulist = self.fromfile(fileobj) try: dirname = os.path.dirname(hdulist._file.name) except (AttributeError, TypeError): dirname = None with _free_space_check(self, dirname=dirname): for hdu in self: hdu._prewriteto(checksum=checksum) hdu._writeto(hdulist._file) hdu._postwriteto() hdulist.close(output_verify=output_verify, closed=closed)
[docs] def close(self, output_verify='exception', verbose=False, closed=True): """ Close the associated FITS file and memmap object, if any. Parameters ---------- output_verify : str Output verification option. Must be one of ``"fix"``, ``"silentfix"``, ``"ignore"``, ``"warn"``, or ``"exception"``. May also be any combination of ``"fix"`` or ``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception" (e.g. ``"fix+warn"``). See :ref:`verify` for more info. verbose : bool When `True`, print out verbose messages. closed : bool When `True`, close the underlying file object. """ try: if (self._file and self._file.mode in ('append', 'update') and not self._file.closed): self.flush(output_verify=output_verify, verbose=verbose) finally: if self._file and closed and hasattr(self._file, 'close'): self._file.close() # Give individual HDUs an opportunity to do on-close cleanup for hdu in self: hdu._close(closed=closed)
[docs] def info(self, output=None): """ Summarize the info of the HDUs in this `HDUList`. Note that this function prints its results to the console---it does not return a value. Parameters ---------- output : file, bool, optional A file-like object to write the output to. If `False`, does not output to a file and instead returns a list of tuples representing the HDU info. Writes to ``sys.stdout`` by default. """ if output is None: output = sys.stdout if self._file is None: name = '(No file associated with this HDUList)' else: name = self._file.name results = [f'Filename: {name}', 'No. Name Ver Type Cards Dimensions Format'] format = '{:3d} {:10} {:3} {:11} {:5d} {} {} {}' default = ('', '', '', 0, (), '', '') for idx, hdu in enumerate(self): summary = hdu._summary() if len(summary) < len(default): summary += default[len(summary):] summary = (idx,) + summary if output: results.append(format.format(*summary)) else: results.append(summary) if output: output.write('\n'.join(results)) output.write('\n') output.flush() else: return results[2:]
[docs] def filename(self): """ Return the file name associated with the HDUList object if one exists. Otherwise returns None. Returns ------- filename : a string containing the file name associated with the HDUList object if an association exists. Otherwise returns None. """ if self._file is not None: if hasattr(self._file, 'name'): return self._file.name return None
@classmethod def _readfrom(cls, fileobj=None, data=None, mode=None, memmap=None, save_backup=False, cache=True, lazy_load_hdus=True, **kwargs): """ Provides the implementations from HDUList.fromfile and HDUList.fromstring, both of which wrap this method, as their implementations are largely the same. """ if fileobj is not None: if not isinstance(fileobj, _File): # instantiate a FITS file object (ffo) fileobj = _File(fileobj, mode=mode, memmap=memmap, cache=cache) # The Astropy mode is determined by the _File initializer if the # supplied mode was None mode = fileobj.mode hdulist = cls(file=fileobj) else: if mode is None: # The default mode mode = 'readonly' hdulist = cls(file=data) # This method is currently only called from HDUList.fromstring and # HDUList.fromfile. If fileobj is None then this must be the # fromstring case; the data type of ``data`` will be checked in the # _BaseHDU.fromstring call. hdulist._save_backup = save_backup hdulist._open_kwargs = kwargs if fileobj is not None and fileobj.writeonly: # Output stream--not interested in reading/parsing # the HDUs--just writing to the output file return hdulist # Make sure at least the PRIMARY HDU can be read read_one = hdulist._read_next_hdu() # If we're trying to read only and no header units were found, # raise an exception if not read_one and mode in ('readonly', 'denywrite'): # Close the file if necessary (issue #6168) if hdulist._file.close_on_error: hdulist._file.close() raise OSError('Empty or corrupt FITS file') if not lazy_load_hdus: # Go ahead and load all HDUs while hdulist._read_next_hdu(): pass # initialize/reset attributes to be used in "update/append" mode hdulist._resize = False hdulist._truncate = False return hdulist def _try_while_unread_hdus(self, func, *args, **kwargs): """ Attempt an operation that accesses an HDU by index/name that can fail if not all HDUs have been read yet. Keep reading HDUs until the operation succeeds or there are no more HDUs to read. """ while True: try: return func(*args, **kwargs) except Exception: if self._read_next_hdu(): continue else: raise def _read_next_hdu(self): """ Lazily load a single HDU from the fileobj or data string the `HDUList` was opened from, unless no further HDUs are found. Returns True if a new HDU was loaded, or False otherwise. """ if self._read_all: return False saved_compression_enabled = compressed.COMPRESSION_ENABLED fileobj, data, kwargs = self._file, self._data, self._open_kwargs if fileobj is not None and fileobj.closed: return False try: self._in_read_next_hdu = True if ('disable_image_compression' in kwargs and kwargs['disable_image_compression']): compressed.COMPRESSION_ENABLED = False # read all HDUs try: if fileobj is not None: try: # Make sure we're back to the end of the last read # HDU if len(self) > 0: last = self[len(self) - 1] if last._data_offset is not None: offset = last._data_offset + last._data_size fileobj.seek(offset, os.SEEK_SET) hdu = _BaseHDU.readfrom(fileobj, **kwargs) except EOFError: self._read_all = True return False except OSError: # Close the file: see # https://github.com/astropy/astropy/issues/6168 # if self._file.close_on_error: self._file.close() if fileobj.writeonly: self._read_all = True return False else: raise else: if not data: self._read_all = True return False hdu = _BaseHDU.fromstring(data, **kwargs) self._data = data[hdu._data_offset + hdu._data_size:] super().append(hdu) if len(self) == 1: # Check for an extension HDU and update the EXTEND # keyword of the primary HDU accordingly self.update_extend() hdu._new = False if 'checksum' in kwargs: hdu._output_checksum = kwargs['checksum'] # check in the case there is extra space after the last HDU or # corrupted HDU except (VerifyError, ValueError) as exc: warnings.warn( 'Error validating header for HDU #{} (note: Astropy ' 'uses zero-based indexing).\n{}\n' 'There may be extra bytes after the last HDU or the ' 'file is corrupted.'.format( len(self), indent(str(exc))), VerifyWarning) del exc self._read_all = True return False finally: compressed.COMPRESSION_ENABLED = saved_compression_enabled self._in_read_next_hdu = False return True def _verify(self, option='warn'): errs = _ErrList([], unit='HDU') # the first (0th) element must be a primary HDU if len(self) > 0 and (not isinstance(self[0], PrimaryHDU)) and \ (not isinstance(self[0], _NonstandardHDU)): err_text = "HDUList's 0th element is not a primary HDU." fix_text = 'Fixed by inserting one as 0th HDU.' def fix(self=self): self.insert(0, PrimaryHDU()) err = self.run_option(option, err_text=err_text, fix_text=fix_text, fix=fix) errs.append(err) if len(self) > 1 and ('EXTEND' not in self[0].header or self[0].header['EXTEND'] is not True): err_text = ('Primary HDU does not contain an EXTEND keyword ' 'equal to T even though there are extension HDUs.') fix_text = 'Fixed by inserting or updating the EXTEND keyword.' def fix(header=self[0].header): naxis = header['NAXIS'] if naxis == 0: after = 'NAXIS' else: after = 'NAXIS' + str(naxis) header.set('EXTEND', value=True, after=after) errs.append(self.run_option(option, err_text=err_text, fix_text=fix_text, fix=fix)) # each element calls their own verify for idx, hdu in enumerate(self): if idx > 0 and (not isinstance(hdu, ExtensionHDU)): err_text = ("HDUList's element {} is not an " "extension HDU.".format(str(idx))) err = self.run_option(option, err_text=err_text, fixable=False) errs.append(err) else: result = hdu._verify(option) if result: errs.append(result) return errs def _flush_update(self): """Implements flushing changes to a file in update mode.""" for hdu in self: # Need to all _prewriteto() for each HDU first to determine if # resizing will be necessary hdu._prewriteto(checksum=hdu._output_checksum, inplace=True) try: self._wasresized() # if the HDUList is resized, need to write out the entire contents of # the hdulist to the file. if self._resize or self._file.compression: self._flush_resize() else: # if not resized, update in place for hdu in self: hdu._writeto(self._file, inplace=True) # reset the modification attributes after updating for hdu in self: hdu._header._modified = False finally: for hdu in self: hdu._postwriteto() def _flush_resize(self): """ Implements flushing changes in update mode when parts of one or more HDU need to be resized. """ old_name = self._file.name old_memmap = self._file.memmap name = _tmp_name(old_name) if not self._file.file_like: old_mode = os.stat(old_name).st_mode # The underlying file is an actual file object. The HDUList is # resized, so we need to write it to a tmp file, delete the # original file, and rename the tmp file to the original file. if self._file.compression == 'gzip': new_file = gzip.GzipFile(name, mode='ab+') elif self._file.compression == 'bzip2': if not HAS_BZ2: raise ModuleNotFoundError( "This Python installation does not provide the bz2 module.") new_file = bz2.BZ2File(name, mode='w') else: new_file = name with self.fromfile(new_file, mode='append') as hdulist: for hdu in self: hdu._writeto(hdulist._file, inplace=True, copy=True) if sys.platform.startswith('win'): # Collect a list of open mmaps to the data; this well be # used later. See below. mmaps = [(idx, _get_array_mmap(hdu.data), hdu.data) for idx, hdu in enumerate(self) if hdu._has_data] hdulist._file.close() self._file.close() if sys.platform.startswith('win'): # Close all open mmaps to the data. This is only necessary on # Windows, which will not allow a file to be renamed or deleted # until all handles to that file have been closed. for idx, mmap, arr in mmaps: if mmap is not None: mmap.close() os.remove(self._file.name) # reopen the renamed new file with "update" mode os.rename(name, old_name) os.chmod(old_name, old_mode) if isinstance(new_file, gzip.GzipFile): old_file = gzip.GzipFile(old_name, mode='rb+') else: old_file = old_name ffo = _File(old_file, mode='update', memmap=old_memmap) self._file = ffo for hdu in self: # Need to update the _file attribute and close any open mmaps # on each HDU if hdu._has_data and _get_array_mmap(hdu.data) is not None: del hdu.data hdu._file = ffo if sys.platform.startswith('win'): # On Windows, all the original data mmaps were closed above. # However, it's possible that the user still has references to # the old data which would no longer work (possibly even cause # a segfault if they try to access it). This replaces the # buffers used by the original arrays with the buffers of mmap # arrays created from the new file. This seems to work, but # it's a flaming hack and carries no guarantees that it won't # lead to odd behavior in practice. Better to just not keep # references to data from files that had to be resized upon # flushing (on Windows--again, this is no problem on Linux). for idx, mmap, arr in mmaps: if mmap is not None: arr.data = self[idx].data.data del mmaps # Just to be sure else: # The underlying file is not a file object, it is a file like # object. We can't write out to a file, we must update the file # like object in place. To do this, we write out to a temporary # file, then delete the contents in our file like object, then # write the contents of the temporary file to the now empty file # like object. self.writeto(name) hdulist = self.fromfile(name) ffo = self._file ffo.truncate(0) ffo.seek(0) for hdu in hdulist: hdu._writeto(ffo, inplace=True, copy=True) # Close the temporary file and delete it. hdulist.close() os.remove(hdulist._file.name) # reset the resize attributes after updating self._resize = False self._truncate = False for hdu in self: hdu._header._modified = False hdu._new = False hdu._file = ffo def _wasresized(self, verbose=False): """ Determine if any changes to the HDUList will require a file resize when flushing the file. Side effect of setting the objects _resize attribute. """ if not self._resize: # determine if any of the HDU is resized for hdu in self: # Header: nbytes = len(str(hdu._header)) if nbytes != (hdu._data_offset - hdu._header_offset): self._resize = True self._truncate = False if verbose: print('One or more header is resized.') break # Data: if not hdu._has_data: continue nbytes = hdu.size nbytes = nbytes + _pad_length(nbytes) if nbytes != hdu._data_size: self._resize = True self._truncate = False if verbose: print('One or more data area is resized.') break if self._truncate: try: self._file.truncate(hdu._data_offset + hdu._data_size) except OSError: self._resize = True self._truncate = False return self._resize