def _get_file_mode(filename, default='copyonwrite'):
"""
Allow file object to already be opened in any of the valid modes and
and leave the file in the same state (opened or closed) as when
the function was called.
"""
mode = default
closed = True
if hasattr(filename, 'closed'):
closed = filename.closed
elif hasattr(filename, 'fileobj') and filename.fileobj is not None:
closed = filename.fileobj.closed
if (isfile(filename) or
isinstance(filename, gzip.GzipFile) and not closed):
if isinstance(filename, gzip.GzipFile):
file_mode = filename.fileobj.mode
else:
file_mode = filename.mode
for key, val in PYTHON_MODES.iteritems():
if val == file_mode:
mode = key
break
return mode, closed
def _open_fileobj(self, fileobj, mode):
"""Open a FITS file from a file object or a GzipFile object."""
closed = fileobj_closed(fileobj)
fmode = fileobj_mode(fileobj) or PYTHON_MODES[mode]
if not closed:
# In some cases (like on Python 3) a file opened for appending
# still shows a mode of 'r+', hence the extra check for the append
# case
if ((mode == 'append' and fmode not in ('ab+', 'rb+')) or
(mode != 'append' and PYTHON_MODES[mode] != fmode)):
raise ValueError(
"Input mode '%s' (%s) does not match mode of the "
"input file (%s)." % (mode, PYTHON_MODES[mode], fmode))
self.__file = fileobj
elif isfile(fileobj):
self.__file = fileobj_open(self.name, PYTHON_MODES[mode])
# Return to the beginning of the file--in Python 3 when opening in
# append mode the file pointer is at the end of the file
self.__file.seek(0)
else:
self.__file = gzip.open(self.name, PYTHON_MODES[mode])
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 for
append (ab+).
output_verify : str
Output verification option. Must be one of ``"fix"``,
``"silentfix"``, ``"ignore"``, ``"warn"``, or
``"exception"``. 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.")
return
self.verify(option=output_verify)
# check if the file object is closed
closed = fileobj_closed(fileobj)
fmode = fileobj_mode(fileobj) or 'ab+'
filename = fileobj_name(fileobj)
# check if the output file already exists
if (isfile(fileobj) or
isinstance(fileobj, (basestring, gzip.GzipFile))):
if (os.path.exists(filename) and os.path.getsize(filename) != 0):
if clobber:
warnings.warn("Overwriting existing file '%s'." % filename)
if not closed:
fileobj.close()
os.remove(filename)
else:
raise IOError("File '%s' already exists." % filename)
elif (hasattr(fileobj, 'len') and fileobj.len > 0):
if clobber:
warnings.warn("Overwriting existing file '%s'." % filename)
name.truncate(0)
else:
raise IOError("File '%s' already exists." % filename)
# make sure the EXTEND keyword is there if there is extension
self.update_extend()
mode = 'copyonwrite'
for key, val in PYTHON_MODES.iteritems():
if val == fmode:
mode = key
break
hdulist = fitsopen(fileobj, mode=mode)
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 __init__(self, fileobj=None, mode='readonly', memmap=False):
if fileobj is None:
self.__file = None
self.closed = False
self.mode = mode
self.memmap = memmap
self.compression = None
self.readonly = False
self.writeonly = False
self.simulateonly = True
return
else:
self.simulateonly = False
if mode not in PYTHON_MODES:
raise ValueError("Mode '%s' not recognized" % mode)
if (isinstance(fileobj, basestring) and mode != 'append' and
not os.path.exists(fileobj) and
not os.path.splitdrive(fileobj)[0]):
#
# Not writing file and file does not exist on local machine and
# name does not begin with a drive letter (Windows), try to
# get it over the web.
#
self.name, _ = urllib.urlretrieve(fileobj)
else:
self.name = fileobj_name(fileobj)
self.closed = False
self.mode = mode
self.memmap = memmap
# Underlying fileobj is a file-like object, but an actual file object
self.file_like = False
# More defaults to be adjusted below as necessary
self.compression = None
self.readonly = False
self.writeonly = False
# Initialize the internal self.__file object
if isfile(fileobj) or isinstance(fileobj, gzip.GzipFile):
closed = fileobj_closed(fileobj)
fmode = fileobj_mode(fileobj) or PYTHON_MODES[mode]
if not closed:
# In some cases (like on Python 3) a file opened for
# appending still shows a mode of 'r+', hence the extra
# check for the append case
if ((mode == 'append' and fmode not in ('ab+', 'rb+')) or
(mode != 'append' and PYTHON_MODES[mode] != fmode)):
raise ValueError(
"Input mode '%s' (%s) does not match mode of the "
"input file (%s)." % (mode, PYTHON_MODES[mode], fmode))
self.__file = fileobj
elif isfile(fileobj):
self.__file = fileobj_open(self.name, PYTHON_MODES[mode])
# Return to the beginning of the file--in Python 3 when
# opening in append mode the file pointer is at the end of
# the file
self.__file.seek(0)
else:
self.__file = gzip.open(self.name, PYTHON_MODES[mode])
elif isinstance(fileobj, basestring):
if os.path.exists(self.name):
with fileobj_open(self.name, 'rb') as f:
magic = f.read(4)
else:
magic = ''.encode('raw-unicode-escape')
ext = os.path.splitext(self.name)[1]
if ext == '.gz' or magic.startswith(GZIP_MAGIC):
# Handle gzip files
if mode in ['update', 'append']:
raise IOError(
"Writing to gzipped fits files is not currently "
"supported")
self.__file = gzip.open(self.name)
self.compression = 'gzip'
elif ext == '.zip' or magic.startswith(PKZIP_MAGIC):
# Handle zip files
if mode in ['update', 'append']:
raise IOError(
"Writing to zipped fits files is not currently "
"supported")
zfile = zipfile.ZipFile(self.name)
namelist = zfile.namelist()
if len(namelist) != 1:
raise IOError(
"Zip files with multiple members are not supported.")
self.__file = tempfile.NamedTemporaryFile(suffix='.fits')
self.__file.write(zfile.read(namelist[0]))
zfile.close()
self.compression = 'zip'
else:
self.__file = fileobj_open(self.name, PYTHON_MODES[mode])
# Make certain we're back at the beginning of the file
self.__file.seek(0)
else:
# We are dealing with a file like object.
# Assume it is open.
self.file_like = True
self.__file = fileobj
# If there is not seek or tell methods then set the mode to
# output streaming.
if (not hasattr(self.__file, 'seek') or
not hasattr(self.__file, 'tell')):
self.mode = mode = 'ostream'
if (self.mode in ('copyonwrite', 'update', 'append') and
not hasattr(self.__file, 'write')):
raise IOError("File-like object does not have a 'write' "
"method, required for mode '%s'."
% self.mode)
if (self.mode in ('readonly', 'denywrite') and
not hasattr(self.__file, 'read')):
raise IOError("File-like object does not have a 'read' "
"method, required for mode %r."
% self.mode)
if isinstance(fileobj, gzip.GzipFile):
self.compression = 'gzip'
elif isinstance(fileobj, zipfile.ZipFile):
# Reading from zip files is supported but not writing (yet)
self.compression = 'zip'
if (mode in ('readonly', 'copyonwrite', 'denywrite') or
(self.compression and mode == 'update')):
self.readonly = True
elif (mode == 'ostream' or
(self.compression and mode == 'append')):
self.writeonly = True
# For 'ab+' mode, the pointer is at the end after the open in
# Linux, but is at the beginning in Solaris.
if (mode == 'ostream' or self.compression or
not hasattr(self.__file, 'seek')):
# For output stream start with a truncated file.
# For compressed files we can't really guess at the size
self.size = 0
else:
pos = self.__file.tell()
self.__file.seek(0, 2)
self.size = self.__file.tell()
self.__file.seek(pos)
if self.memmap and not isfile(self.__file):
self.memmap = False
def __init__(self, fileobj=None, mode='readonly', memmap=False):
if fileobj is None:
self.__file = None
self.closed = False
self.mode = mode
self.memmap = memmap
self.compression = None
self.readonly = False
self.writeonly = False
self.simulateonly = True
return
else:
self.simulateonly = False
if mode not in PYTHON_MODES:
raise ValueError("Mode '%s' not recognized" % mode)
if (isinstance(fileobj, basestring) and mode != 'append' and
not os.path.exists(fileobj) and
not os.path.splitdrive(fileobj)[0]):
#
# Not writing file and file does not exist on local machine and
# name does not begin with a drive letter (Windows), try to
# get it over the web.
#
try:
self.name, _ = urllib.urlretrieve(fileobj)
except (TypeError, ValueError):
# A couple different exceptions can occur here when passing a
# filename into urlretrieve in Python 3
raise IOError('File does not exist: %r' % fileobj)
else:
self.name = fileobj_name(fileobj)
self.closed = False
self.mode = mode
self.memmap = memmap
# Underlying fileobj is a file-like object, but an actual file object
self.file_like = False
# More defaults to be adjusted below as necessary
self.compression = None
self.readonly = False
self.writeonly = False
# Initialize the internal self.__file object
if isfile(fileobj) or isinstance(fileobj, gzip.GzipFile):
self._open_fileobj(fileobj, mode)
elif isinstance(fileobj, basestring):
self._open_filename(fileobj, mode)
else:
self._open_filelike(fileobj, mode)
if isinstance(fileobj, gzip.GzipFile):
self.compression = 'gzip'
elif isinstance(fileobj, zipfile.ZipFile):
# Reading from zip files is supported but not writing (yet)
self.compression = 'zip'
if (mode in ('readonly', 'copyonwrite', 'denywrite') or
(self.compression and mode == 'update')):
self.readonly = True
elif (mode == 'ostream' or
(self.compression and mode == 'append')):
self.writeonly = True
# For 'ab+' mode, the pointer is at the end after the open in
# Linux, but is at the beginning in Solaris.
if (mode == 'ostream' or self.compression or
not hasattr(self.__file, 'seek')):
# For output stream start with a truncated file.
# For compressed files we can't really guess at the size
self.size = 0
else:
pos = self.__file.tell()
self.__file.seek(0, 2)
self.size = self.__file.tell()
self.__file.seek(pos)
if self.memmap and not isfile(self.__file):
self.memmap = False