# 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,
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.
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.
"""
if memmap is None:
from .. import conf
# 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']
if not name:
raise ValueError('Empty filename: %s' % repr(name))
return HDUList.fromfile(name, mode, memmap, save_backup, cache, **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, 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
[docs] 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
[docs] 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)
[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
[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('%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()
[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(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()
[docs] 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
[docs] def readall(self):
"""
Read data of all HDUs into memory.
"""
for hdu in self:
if hdu.data is not None:
continue
@ignore_sigint
[docs] 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()
[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
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))
[docs] 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)
[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.
"""
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)
[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 = ['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:]
[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, **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+')
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