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

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

    from __future__ import print_function

    import gzip
    import os
    import shutil
    import sys
    import warnings

    from . import compressed
    from .base import _BaseHDU, _ValidHDU, _NonstandardHDU, ExtensionHDU
    from .groups import GroupsHDU
    from .image import PrimaryHDU, ImageHDU
    from ..file import _File
    from ..header import _pad_length
    from ..util import (_is_int, _tmp_name, fileobj_closed, ignore_sigint,
                        _get_array_mmap)
    from ..verify import _Verify, _ErrList, VerifyError, VerifyWarning
    from ....extern.six import string_types
    from ....utils import indent
    from ....utils.exceptions import AstropyUserWarning, AstropyDeprecationWarning

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

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

        mode : str, optional
            Open mode, 'readonly' (default), 'update', 'append', 'denywrite', or
            'ostream'.

            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?

        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.

        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: `True`).

        kwargs : dict, optional
            additional optional keyword arguments, possible values are:

            - **uint** : bool

                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.
                This is enabled by default so that the pseudo-unsigned
                integer convention is assumed.

                Note, for backward compatibility, the kwarg **uint16** may
                be used instead.  The kwarg was renamed when support was
                added for integers of any size.

            - **ignore_missing_end** : bool

                Do not issue an exception when opening a file that is
                missing an ``END`` card in the last header.

            - **checksum** : bool, str

                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.

            - **disable_image_compression** : bool

                If `True`, treats compressed image HDU's like normal
                binary table HDU's.

            - **do_not_scale_image_data** : bool

                If `True`, image data is not scaled using BSCALE/BZERO values
                when read.

            - **ignore_blank** : bool
               If `True`, the BLANK keyword is ignored if present.

            - **scale_back** : bool

                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.

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

        """

        from .. 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 'uint16' in kwargs and 'uint' not in kwargs:
            kwargs['uint'] = kwargs['uint16']
            del kwargs['uint16']
            warnings.warn(
                'The uint16 keyword argument is deprecated since v1.1.0.  Use '
                'the uint argument instead.', AstropyDeprecationWarning)

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

        if not name:
            raise ValueError('Empty filename: %s' % repr(name))

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

    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, optional
                The opened physical file associated with the `HDUList`.
            """

            self._file = file
            self._save_backup = 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 %d in the HDUList input is not an HDU." % idx)

            super(HDUList, self).__init__(hdus)

            self.update_extend()

        def __iter__(self):
            for idx in range(len(self)):
                yield self[idx]

        def __getitem__(self, key):
            """
            Get an HDU from the `HDUList`, indexed by number or name.
            """

            if isinstance(key, slice):
                hdus = super(HDUList, self).__getitem__(key)
                return HDUList(hdus)

            idx = self.index_of(key)
            return super(HDUList, self).__getitem__(idx)

        def __contains__(self, item):
            """
            Returns `True` if ``HDUList.index_of(item)`` succeeds.
            """
            try:
                self.index_of(item)
                return True
            except KeyError:
                return False

        def __setitem__(self, key, hdu):
            """
            Set an HDU to the `HDUList`, indexed by number or name.
            """

            _key = self.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('%s is not an HDU.' % item)
            else:
                if not isinstance(hdu, _BaseHDU):
                    raise ValueError('%s is not an HDU.' % hdu)

            try:
                super(HDUList, self).__setitem__(_key, hdu)
            except IndexError:
                raise IndexError('Extension %s is out of bound or not found.'
                                 % 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.index_of(key)
                end_index = len(self) - 1

            super(HDUList, self).__delitem__(key)

            if (key == end_index or key == -1 and not self._resize):
                self._truncate = True
            else:
                self._truncate = False
                self._resize = True

        def __getslice__(self, start, end):
            return self[slice(start, end)]

        def __delslice__(self, start, stop):
            """
            Delete a slice of HDUs from the `HDUList`, indexed by number only.
            """

            del self[slice(start, stop)]

        # Support the 'with' statement
        def __enter__(self):
            return self

        def __exit__(self, type, value, traceback):
            self.close()

        @classmethod
        def fromfile(cls, fileobj, mode=None, memmap=None,
                     save_backup=False, cache=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, **kwargs)

        @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.
            """

            return cls._readfrom(data=data, **kwargs)

        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 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('%s is not an HDU.' % 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(HDUList, self).insert(1, hdu1)
                    super(HDUList, self).__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(HDUList, self).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(HDUList, self).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()

        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(HDUList, self).append(phdu)

            super(HDUList, self).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()

        def index_of(self, key):
            """
            Get the index of an HDU from the `HDUList`.

            Parameters
            ----------
            key : int, str or tuple of (string, int)
               The key identifying the HDU.  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.

            Returns
            -------
            index : int
               The index of the HDU in the `HDUList`.
            """

            if _is_int(key):
                return key
            elif isinstance(key, tuple):
                _key, _ver = key
            else:
                _key = key
                _ver = None

            if not isinstance(_key, string_types):
                raise KeyError(key)
            _key = (_key.strip()).upper()

            nfound = 0
            found = None
            for idx, hdu in enumerate(self):
                name = hdu.name
                if isinstance(name, string_types):
                    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
                    nfound += 1

            if (nfound == 0):
                raise KeyError('Extension %s not found.' % repr(key))
            elif (nfound > 1):
                raise KeyError('There are %d extensions of %s.'
                               % (nfound, repr(key)))
            else:
                return found

        def readall(self):
            """
            Read data of all HDUs into memory.
            """

            for hdu in self:
                if hdu.data is not None:
                    continue

        @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 '%s' mode is not supported."
                              % 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 %s to %s.' %
                                  (filename, backup), AstropyUserWarning)
                    try:
                        shutil.copy(filename, backup)
                    except IOError as exc:
                        raise IOError('Failed to save backup to destination %s: '
                                      '%s' % (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)
                        try:
                            hdu._writeto(self._file)
                            if verbose:
                                print('append HDU', hdu.name, extver)
                            hdu._new = False
                        finally:
                            hdu._postwriteto()
            elif self._file.mode == 'update':
                self._flush_update()

        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

            if 'EXTEND' in hdr:
                if len(self) > 1 and hdr['EXTEND'] == False:
                    hdr['EXTEND'] = True
            elif len(self) > 1:
                if hdr['NAXIS'] == 0:
                    hdr.set('EXTEND', True, after='NAXIS')
                else:
                    n = hdr['NAXIS']
                    hdr.set('EXTEND', True, after='NAXIS' + str(n))

        def writeto(self, fileobj, output_verify='exception', clobber=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.

            clobber : bool
                When `True`, overwrite the output file if exists.

            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, string_types) or fileobj_closed(fileobj)

            # writeto is only for writing a new file from scratch, so the most
            # sensible mode to require is '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='ostream', clobber=clobber)
            hdulist = self.fromfile(fileobj)

            for hdu in self:
                hdu._prewriteto(checksum=checksum)
                try:
                    hdu._writeto(hdulist._file)
                finally:
                    hdu._postwriteto()

            hdulist.close(output_verify=output_verify, closed=closed)

        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.
            """

            if self._file:
                if self._file.mode in ['append', 'update']:
                    self.flush(output_verify=output_verify, verbose=verbose)

                if 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)

        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 = ['Filename: %s' % name,
                       'No.    Name         Type      Cards   Dimensions   Format']

            format = '%-3d  %-10s  %-11s  %5d   %-10s   %s   %s'
            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 % summary)
                else:
                    results.append(summary)

            if output:
                output.write('\n'.join(results))
                output.write('\n')
                output.flush()
            else:
                return results[2:]

        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, **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)
                    ffo = _File(fileobj, mode=mode, memmap=memmap, cache=cache)
                else:
                    ffo = fileobj
                # The pyfits mode is determined by the _File initializer if the
                # supplied mode was None
                mode = ffo.mode
                hdulist = cls(file=ffo)
            else:
                if mode is None:
                    # The default mode
                    mode = 'readonly'

                hdulist = cls()
                # 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

            saved_compression_enabled = compressed.COMPRESSION_ENABLED

            try:
                if ('disable_image_compression' in kwargs and
                    kwargs['disable_image_compression']):
                    compressed.COMPRESSION_ENABLED = False

                # read all HDUs
                while True:
                    try:
                        if fileobj is not None:
                            if ffo.writeonly:
                                # Output stream--not interested in reading/parsing
                                # the HDUs--just writing to the output file
                                return hdulist

                            try:
                                hdu = _BaseHDU.readfrom(ffo, **kwargs)
                            except EOFError:
                                break
                            except IOError:
                                if ffo.writeonly:
                                    break
                                else:
                                    raise
                        else:
                            if not data:
                                break
                            hdu = _BaseHDU.fromstring(data)
                            data = data[hdu._data_offset + hdu._data_size:]
                        hdulist.append(hdu)
                        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 #%d (note: Astropy '
                            'uses zero-based indexing).\n%s\n'
                            'There may be extra bytes after the last HDU or the '
                            'file is corrupted.' %
                            (len(hdulist), indent(str(exc))), VerifyWarning)
                        del exc
                        break

                # If we're trying to read only and no header units were found,
                # raise and exception
                if mode in ('readonly', 'denywrite') and len(hdulist) == 0:
                    raise IOError('Empty or corrupt FITS file')

                # initialize/reset attributes to be used in "update/append" mode
                hdulist._resize = False
                hdulist._truncate = False

            finally:
                compressed.COMPRESSION_ENABLED = saved_compression_enabled

            return hdulist

        def _verify(self, option='warn'):
            text = ''
            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 %s is not an extension HDU." %
                                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':
                    new_file = bz2.BZ2File(name, mode='w')
                else:
                    new_file = name

                hdulist = self.fromfile(new_file, mode='append')

                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 IOError:
                        self._resize = True
                    self._truncate = False

            return self._resize