# 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 def fitsopen(name, mode='readonly', memmap=None, save_backup=False, **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 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 Is memory mapping to be used? save_backup : bool 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. kwargs : dict 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. 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`, treates 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. """ if memmap is None: from .. import conf memmap = conf.use_memmap if 'uint16' in kwargs and 'uint' not in kwargs: kwargs['uint'] = kwargs['uint16'] del kwargs['uint16'] if not name: raise ValueError('Empty filename: %s' % repr(name)) return HDUList.fromfile(name, mode, memmap, save_backup, **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 __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=False, save_backup=False, **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, **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() 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=False, save_backup=False, **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) 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 acutal 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+') 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