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$ python setup.py test -V -t gammapy/datasets/tests/test_load.py --remote-data
running test
running build
running build_py
running build_scripts
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/tests/helper.py:30: UserWarning: Module gammapy was already imported from gammapy/__init__.pyc, but /Users/deil/Library/Python/2.7/lib/python/site-packages/gammapy-0.1-py2.7.egg is being added to sys.path
import pkg_resources
========================================================== test session starts ==========================================================
platform darwin -- Python 2.7.8 -- pytest-2.5.1 -- /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
cachedir: /private/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/gammapy-test-lhkkyp/lib.macosx-10.9-x86_64-2.7/.cache
Running tests with Astropy version 0.4rc3.dev9437.
Running tests in /private/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/gammapy-test-lhkkyp/lib.macosx-10.9-x86_64-2.7/gammapy/datasets/tests/test_load.py.
Platform: Darwin-13.3.0-x86_64-i386-64bit
Executable: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Full Python Version:
2.7.8 (default, Jul 13 2014, 17:11:32)
[GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.40)]
encodings: sys: ascii, locale: UTF-8, filesystem: utf-8, unicode bits: 15
byteorder: little
float info: dig: 15, mant_dig: 15
Numpy: 1.8.1
Scipy: 0.14.0
Matplotlib: 1.3.1
h5py: 2.3.1
Using Astropy options: remote_data.
plugins: bench, cache, cov, pep8, rerunfailures, xdist
collected 13 items
gammapy/datasets/tests/test_load.py:14: test_poisson_stats_image PASSED
gammapy/datasets/tests/test_load.py:20: test_poisson_stats_image_direct PASSED
gammapy/datasets/tests/test_load.py:27: test_poisson_stats_extra_info PASSED
gammapy/datasets/tests/test_load.py:36: TestFermiGalacticCenter.test_filenames PASSED
gammapy/datasets/tests/test_load.py:40: TestFermiGalacticCenter.test_psf PASSED
gammapy/datasets/tests/test_load.py:45: TestFermiGalacticCenter.test_counts PASSED
gammapy/datasets/tests/test_load.py:50: TestFermiGalacticCenter.test_diffuse_model PASSED
gammapy/datasets/tests/test_load.py:56: TestFermiGalacticCenter.test_exposure_cube XPASS
gammapy/datasets/tests/test_load.py:65: TestFermiVelaRegion.test_filenames PASSED
gammapy/datasets/tests/test_load.py:70: TestFermiVelaRegion.test_counts FAILED
gammapy/datasets/tests/test_load.py:76: TestFermiVelaRegion.test_background_cube FAILED
gammapy/datasets/tests/test_load.py:82: TestFermiVelaRegion.test_exposure_cube FAILED
gammapy/datasets/tests/test_load.py:90: test_fetch_fermi_catalog PASSED
=============================================================== FAILURES ================================================================
____________________________________________________ TestFermiVelaRegion.test_counts ____________________________________________________
self = <gammapy.datasets.tests.test_load.TestFermiVelaRegion instance at 0x1042e42d8>
@remote_data
def test_counts(self):
> counts = FermiVelaRegion.counts()
gammapy/datasets/tests/test_load.py:72:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
@staticmethod
def counts():
"""Counts image as `astropy.io.fits.ImageHDU`."""
filename = FermiVelaRegion.filenames()['counts']
> return fits.open(filename)[0]
gammapy/datasets/load.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/7671c309f1222e98f49c724177107624'
mode = 'readonly', memmap = True, save_backup = False, kwargs = {}, conf = <astropy.io.fits.Conf object at 0x103049150>
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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.hdulist.HDUList'>
fileobj = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/7671c309f1222e98f49c724177107624'
mode = 'readonly', memmap = True, save_backup = False, kwargs = {}
@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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:251:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.hdulist.HDUList'>
fileobj = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/7671c309f1222e98f49c724177107624'
data = None, mode = 'readonly', memmap = True, save_backup = False, kwargs = {}
ffo = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/7671c309f1222e98f49c724177107624', mode 'rb' at 0x1042b5300>>
hdulist = [], saved_compression_enabled = True
@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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:805:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.base._BaseHDU'>
fileobj = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/7671c309f1222e98f49c724177107624', mode 'rb' at 0x1042b5300>>
checksum = False, ignore_missing_end = False, kwargs = {}
@classmethod
def readfrom(cls, fileobj, checksum=False, ignore_missing_end=False,
**kwargs):
"""
Read the HDU from a file. Normally an HDU should be opened with
:func:`open` which reads the entire HDU list in a FITS file. But this
method is still provided for symmetry with :func:`writeto`.
Parameters
----------
fileobj : file object or file-like object
Input FITS file. The file's seek pointer is assumed to be at the
beginning of the HDU.
checksum : bool
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.
ignore_missing_end : bool
Do not issue an exception when opening a file that is missing an
``END`` card in the last header.
"""
# TODO: Figure out a way to make it possible for the _File
# constructor to be a noop if the argument is already a _File
if not isinstance(fileobj, _File):
fileobj = _File(fileobj)
hdu = cls._readfrom_internal(fileobj, checksum=checksum,
ignore_missing_end=ignore_missing_end,
> **kwargs)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/base.py:379:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.base._BaseHDU'>
data = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/7671c309f1222e98f49c724177107624', mode 'rb' at 0x1042b5300>>
header = None, checksum = False, ignore_missing_end = False, kwargs = {}, hdu_buffer = None, hdu_fileobj = None, header_offset = 0
from_file = True
@classmethod
def _readfrom_internal(cls, data, header=None, checksum=False,
ignore_missing_end=False, **kwargs):
"""
Provides the bulk of the internal implementation for readfrom and
fromstring.
For some special cases, supports using a header that was already
created, and just using the input data for the actual array data.
"""
hdu_buffer = None
hdu_fileobj = None
header_offset = 0
if isinstance(data, _File):
from_file = True
if header is None:
header_offset = data.tell()
> header = Header.fromfile(data, endcard=not ignore_missing_end)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/base.py:439:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.header.Header'>
fileobj = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/7671c309f1222e98f49c724177107624', mode 'rb' at 0x1042b5300>>
sep = '', endcard = True, padding = True
@classmethod
def fromfile(cls, fileobj, sep='', endcard=True, padding=True):
"""
Similar to :meth:`Header.fromstring`, but reads the header string from
a given file-like object or filename.
Parameters
----------
fileobj : str, file-like
A filename or an open file-like object from which a FITS header is
to be read. For open file handles the file pointer must be at the
beginning of the header.
sep : str, optional
The string separating cards from each other, such as a newline. By
default there is no card separator (as is the case in a raw FITS
file).
endcard : bool, optional
If True (the default) the header must end with an END card in order
to be considered valid. If an END card is not found an
`~.exceptions.IOError` is raised.
padding : bool, optional
If True (the default) the header will be required to be padded out
to a multiple of 2880, the FITS header block size. Otherwise any
padding, or lack thereof, is ignored.
Returns
-------
header
A new `Header` instance.
"""
close_file = False
if isinstance(fileobj, string_types):
# Open in text mode by default to support newline handling; if a
# binary-mode file object is passed in, the user is on their own
# with respect to newline handling
fileobj = open(fileobj, 'r')
close_file = True
try:
is_binary = fileobj_is_binary(fileobj)
def block_iter(nbytes):
while True:
data = fileobj.read(nbytes)
if data:
yield data
else:
break
return cls._from_blocks(block_iter, is_binary, sep, endcard,
> padding)[1]
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/header.py:462:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.header.Header'>, block_iter = <function block_iter at 0x104323398>, is_binary = True, sep = ''
endcard = True, padding = True
@classmethod
def _from_blocks(cls, block_iter, is_binary, sep, endcard, padding):
"""
The meat of `Header.fromfile`; in a separate method so that
`Header.fromfile` itself is just responsible for wrapping file
handling. Also used by `_BaseHDU.fromstring`.
``block_iter`` should be a callable which, given a block size n
(typically 2880 bytes as used by the FITS standard) returns an iterator
of byte strings of that block size.
``is_binary`` specifies whether the returned blocks are bytes or text
Returns both the entire header *string*, and the `Header` object
returned by Header.fromstring on that string.
"""
actual_block_size = _block_size(sep)
clen = Card.length + len(sep)
blocks = block_iter(actual_block_size)
# Read the first header block.
try:
block = next(blocks)
except StopIteration:
raise EOFError()
if not is_binary:
# TODO: There needs to be error handling at *this* level for
# non-ASCII characters; maybe at this stage decoding latin-1 might
# be safer
block = encode_ascii(block)
read_blocks = []
is_eof = False
end_found = False
# continue reading header blocks until END card or EOF is reached
while True:
# find the END card
end_found, block = cls._find_end_card(block, clen)
read_blocks.append(decode_ascii(block))
if end_found:
break
try:
block = next(blocks)
except StopIteration:
is_eof = True
break
if not block:
is_eof = True
break
if not is_binary:
block = encode_ascii(block)
if not end_found and is_eof and endcard:
# TODO: Pass this error to validation framework as an ERROR,
# rather than raising an exception
> raise IOError('Header missing END card.')
E IOError: Header missing END card.
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/header.py:531: IOError
_______________________________________________ TestFermiVelaRegion.test_background_cube ________________________________________________
self = <gammapy.datasets.tests.test_load.TestFermiVelaRegion instance at 0x104610248>
@remote_data
def test_background_cube(self):
> background = FermiVelaRegion.background_cube()
gammapy/datasets/tests/test_load.py:78:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
@staticmethod
def background_cube():
"""Predicted background counts spectral cube, based on the Fermi Diffuse model.
Returns
-------
spectral_cube : `~gammapy.spectral_cube.GammaSpectralCube`
Diffuse model spectral cube
"""
filename = FermiVelaRegion.filenames()['background_cube']
> return fits.open(filename)[0]
gammapy/datasets/load.py:213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/b856f8f907ea3a897d109bcee42bf7e0'
mode = 'readonly', memmap = True, save_backup = False, kwargs = {}, conf = <astropy.io.fits.Conf object at 0x103049150>
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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.hdulist.HDUList'>
fileobj = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/b856f8f907ea3a897d109bcee42bf7e0'
mode = 'readonly', memmap = True, save_backup = False, kwargs = {}
@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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:251:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.hdulist.HDUList'>
fileobj = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/b856f8f907ea3a897d109bcee42bf7e0'
data = None, mode = 'readonly', memmap = True, save_backup = False, kwargs = {}
ffo = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/b856f8f907ea3a897d109bcee42bf7e0', mode 'rb' at 0x1042b54b0>>
hdulist = [], saved_compression_enabled = True
@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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:805:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.base._BaseHDU'>
fileobj = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/b856f8f907ea3a897d109bcee42bf7e0', mode 'rb' at 0x1042b54b0>>
checksum = False, ignore_missing_end = False, kwargs = {}
@classmethod
def readfrom(cls, fileobj, checksum=False, ignore_missing_end=False,
**kwargs):
"""
Read the HDU from a file. Normally an HDU should be opened with
:func:`open` which reads the entire HDU list in a FITS file. But this
method is still provided for symmetry with :func:`writeto`.
Parameters
----------
fileobj : file object or file-like object
Input FITS file. The file's seek pointer is assumed to be at the
beginning of the HDU.
checksum : bool
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.
ignore_missing_end : bool
Do not issue an exception when opening a file that is missing an
``END`` card in the last header.
"""
# TODO: Figure out a way to make it possible for the _File
# constructor to be a noop if the argument is already a _File
if not isinstance(fileobj, _File):
fileobj = _File(fileobj)
hdu = cls._readfrom_internal(fileobj, checksum=checksum,
ignore_missing_end=ignore_missing_end,
> **kwargs)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/base.py:379:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.base._BaseHDU'>
data = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/b856f8f907ea3a897d109bcee42bf7e0', mode 'rb' at 0x1042b54b0>>
header = None, checksum = False, ignore_missing_end = False, kwargs = {}, hdu_buffer = None, hdu_fileobj = None, header_offset = 0
from_file = True
@classmethod
def _readfrom_internal(cls, data, header=None, checksum=False,
ignore_missing_end=False, **kwargs):
"""
Provides the bulk of the internal implementation for readfrom and
fromstring.
For some special cases, supports using a header that was already
created, and just using the input data for the actual array data.
"""
hdu_buffer = None
hdu_fileobj = None
header_offset = 0
if isinstance(data, _File):
from_file = True
if header is None:
header_offset = data.tell()
> header = Header.fromfile(data, endcard=not ignore_missing_end)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/base.py:439:
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cls = <class 'astropy.io.fits.header.Header'>
fileobj = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/b856f8f907ea3a897d109bcee42bf7e0', mode 'rb' at 0x1042b54b0>>
sep = '', endcard = True, padding = True
@classmethod
def fromfile(cls, fileobj, sep='', endcard=True, padding=True):
"""
Similar to :meth:`Header.fromstring`, but reads the header string from
a given file-like object or filename.
Parameters
----------
fileobj : str, file-like
A filename or an open file-like object from which a FITS header is
to be read. For open file handles the file pointer must be at the
beginning of the header.
sep : str, optional
The string separating cards from each other, such as a newline. By
default there is no card separator (as is the case in a raw FITS
file).
endcard : bool, optional
If True (the default) the header must end with an END card in order
to be considered valid. If an END card is not found an
`~.exceptions.IOError` is raised.
padding : bool, optional
If True (the default) the header will be required to be padded out
to a multiple of 2880, the FITS header block size. Otherwise any
padding, or lack thereof, is ignored.
Returns
-------
header
A new `Header` instance.
"""
close_file = False
if isinstance(fileobj, string_types):
# Open in text mode by default to support newline handling; if a
# binary-mode file object is passed in, the user is on their own
# with respect to newline handling
fileobj = open(fileobj, 'r')
close_file = True
try:
is_binary = fileobj_is_binary(fileobj)
def block_iter(nbytes):
while True:
data = fileobj.read(nbytes)
if data:
yield data
else:
break
return cls._from_blocks(block_iter, is_binary, sep, endcard,
> padding)[1]
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/header.py:462:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.header.Header'>, block_iter = <function block_iter at 0x105a85cf8>, is_binary = True, sep = ''
endcard = True, padding = True
@classmethod
def _from_blocks(cls, block_iter, is_binary, sep, endcard, padding):
"""
The meat of `Header.fromfile`; in a separate method so that
`Header.fromfile` itself is just responsible for wrapping file
handling. Also used by `_BaseHDU.fromstring`.
``block_iter`` should be a callable which, given a block size n
(typically 2880 bytes as used by the FITS standard) returns an iterator
of byte strings of that block size.
``is_binary`` specifies whether the returned blocks are bytes or text
Returns both the entire header *string*, and the `Header` object
returned by Header.fromstring on that string.
"""
actual_block_size = _block_size(sep)
clen = Card.length + len(sep)
blocks = block_iter(actual_block_size)
# Read the first header block.
try:
block = next(blocks)
except StopIteration:
raise EOFError()
if not is_binary:
# TODO: There needs to be error handling at *this* level for
# non-ASCII characters; maybe at this stage decoding latin-1 might
# be safer
block = encode_ascii(block)
read_blocks = []
is_eof = False
end_found = False
# continue reading header blocks until END card or EOF is reached
while True:
# find the END card
end_found, block = cls._find_end_card(block, clen)
read_blocks.append(decode_ascii(block))
if end_found:
break
try:
block = next(blocks)
except StopIteration:
is_eof = True
break
if not block:
is_eof = True
break
if not is_binary:
block = encode_ascii(block)
if not end_found and is_eof and endcard:
# TODO: Pass this error to validation framework as an ERROR,
# rather than raising an exception
> raise IOError('Header missing END card.')
E IOError: Header missing END card.
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/header.py:531: IOError
________________________________________________ TestFermiVelaRegion.test_exposure_cube _________________________________________________
self = <gammapy.datasets.tests.test_load.TestFermiVelaRegion instance at 0x105d2a7e8>
@remote_data
def test_exposure_cube(self):
> exposure_cube = FermiVelaRegion.exposure_cube()
gammapy/datasets/tests/test_load.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
@staticmethod
def exposure_cube():
"""Exposure cube.
Returns
-------
spectral_cube : `~gammapy.spectral_cube.GammaSpectralCube`
Exposure cube
"""
filename = FermiVelaRegion.filenames()['exposure_cube']
> return GammaSpectralCube.read(filename)
gammapy/datasets/load.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/042f15bfd69d3d3153427aeb62d52f8f'
@staticmethod
def read(filename):
"""Read spectral cube from FITS file.
Parameters
----------
filename : str
File name
Returns
-------
spectral_cube : `GammaSpectralCube`
Spectral cube
"""
> data = fits.getdata(filename)
gammapy/spectral_cube/core.py:136:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/042f15bfd69d3d3153427aeb62d52f8f'
args = (), kwargs = {}, mode = 'readonly', closed = False, header = None, lower = None, upper = None, view = None
def getdata(filename, *args, **kwargs):
"""
Get the data from an extension of a FITS file (and optionally the
header).
Parameters
----------
filename : file path, file object, or file like object
File to get data from. If opened, mode must be one of the
following rb, rb+, or ab+.
ext
The rest of the arguments are for extension specification.
They are flexible and are best illustrated by examples.
No extra arguments implies the primary header::
getdata('in.fits')
By extension number::
getdata('in.fits', 0) # the primary header
getdata('in.fits', 2) # the second extension
getdata('in.fits', ext=2) # the second extension
By name, i.e., ``EXTNAME`` value (if unique)::
getdata('in.fits', 'sci')
getdata('in.fits', extname='sci') # equivalent
Note ``EXTNAME`` values are not case sensitive
By combination of ``EXTNAME`` and EXTVER`` as separate
arguments or as a tuple::
getdata('in.fits', 'sci', 2) # EXTNAME='SCI' & EXTVER=2
getdata('in.fits', extname='sci', extver=2) # equivalent
getdata('in.fits', ('sci', 2)) # equivalent
Ambiguous or conflicting specifications will raise an exception::
getdata('in.fits', ext=('sci',1), extname='err', extver=2)
header : bool, optional
If `True`, return the data and the header of the specified HDU as a
tuple.
lower, upper : bool, optional
If ``lower`` or ``upper`` are `True`, the field names in the
returned data object will be converted to lower or upper case,
respectively.
view : ndarray, optional
When given, the data will be returned wrapped in the given ndarray
subclass by calling::
data.view(view)
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
Returns
-------
array : array, record array or groups data object
Type depends on the type of the extension being referenced.
If the optional keyword ``header`` is set to `True`, this
function will return a (``data``, ``header``) tuple.
"""
mode, closed = _get_file_mode(filename)
header = kwargs.pop('header', None)
lower = kwargs.pop('lower', None)
upper = kwargs.pop('upper', None)
view = kwargs.pop('view', None)
> hdulist, extidx = _getext(filename, mode, *args, **kwargs)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/convenience.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/042f15bfd69d3d3153427aeb62d52f8f'
mode = 'readonly', args = (), kwargs = {}, ext = 0, extname = None, extver = None
err_msg = "Redundant/conflicting extension arguments(s): {'ext': None, 'args': (), 'extver': None, 'extname': None}"
def _getext(filename, mode, *args, **kwargs):
"""
Open the input file, return the `HDUList` and the extension.
This supports several different styles of extension selection. See the
:func:`getdata()` documentation for the different possibilities.
"""
ext = kwargs.pop('ext', None)
extname = kwargs.pop('extname', None)
extver = kwargs.pop('extver', None)
err_msg = ('Redundant/conflicting extension arguments(s): %s' %
({'args': args, 'ext': ext, 'extname': extname,
'extver': extver},))
# This code would be much simpler if just one way of specifying an
# extension were picked. But now we need to support all possible ways for
# the time being.
if len(args) == 1:
# Must be either an extension number, an extension name, or an
# (extname, extver) tuple
if _is_int(args[0]) or (isinstance(ext, tuple) and len(ext) == 2):
if ext is not None or extname is not None or extver is not None:
raise TypeError(err_msg)
ext = args[0]
elif isinstance(args[0], string_types):
# The first arg is an extension name; it could still be valid
# to provide an extver kwarg
if ext is not None or extname is not None:
raise TypeError(err_msg)
extname = args[0]
else:
# Take whatever we have as the ext argument; we'll validate it
# below
ext = args[0]
elif len(args) == 2:
# Must be an extname and extver
if ext is not None or extname is not None or extver is not None:
raise TypeError(err_msg)
extname = args[0]
extver = args[1]
elif len(args) > 2:
raise TypeError('Too many positional arguments.')
if (ext is not None and
not (_is_int(ext) or
(isinstance(ext, tuple) and len(ext) == 2 and
isinstance(ext[0], string_types) and _is_int(ext[1])))):
raise ValueError(
'The ext keyword must be either an extension number '
'(zero-indexed) or a (extname, extver) tuple.')
if extname is not None and not isinstance(extname, string_types):
raise ValueError('The extname argument must be a string.')
if extver is not None and not _is_int(extver):
raise ValueError('The extver argument must be an integer.')
if ext is None and extname is None and extver is None:
ext = 0
elif ext is not None and (extname is not None or extver is not None):
raise TypeError(err_msg)
elif extname:
if extver:
ext = (extname, extver)
else:
ext = (extname, 1)
elif extver and extname is None:
raise TypeError('extver alone cannot specify an extension.')
> hdulist = fitsopen(filename, mode=mode, **kwargs)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/convenience.py:753:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/042f15bfd69d3d3153427aeb62d52f8f'
mode = 'readonly', memmap = True, save_backup = False, kwargs = {}, conf = <astropy.io.fits.Conf object at 0x103049150>
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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.hdulist.HDUList'>
fileobj = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/042f15bfd69d3d3153427aeb62d52f8f'
mode = 'readonly', memmap = True, save_backup = False, kwargs = {}
@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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:251:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.hdulist.HDUList'>
fileobj = '/var/folders/sb/4qv5j4m90pz1rw7m70rj1b1r0000gn/T/tmpna45hsastropy_cache/astropy/download/042f15bfd69d3d3153427aeb62d52f8f'
data = None, mode = 'readonly', memmap = True, save_backup = False, kwargs = {}
ffo = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/042f15bfd69d3d3153427aeb62d52f8f', mode 'rb' at 0x1042b5420>>
hdulist = [], saved_compression_enabled = True
@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)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/hdulist.py:805:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.base._BaseHDU'>
fileobj = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/042f15bfd69d3d3153427aeb62d52f8f', mode 'rb' at 0x1042b5420>>
checksum = False, ignore_missing_end = False, kwargs = {}
@classmethod
def readfrom(cls, fileobj, checksum=False, ignore_missing_end=False,
**kwargs):
"""
Read the HDU from a file. Normally an HDU should be opened with
:func:`open` which reads the entire HDU list in a FITS file. But this
method is still provided for symmetry with :func:`writeto`.
Parameters
----------
fileobj : file object or file-like object
Input FITS file. The file's seek pointer is assumed to be at the
beginning of the HDU.
checksum : bool
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.
ignore_missing_end : bool
Do not issue an exception when opening a file that is missing an
``END`` card in the last header.
"""
# TODO: Figure out a way to make it possible for the _File
# constructor to be a noop if the argument is already a _File
if not isinstance(fileobj, _File):
fileobj = _File(fileobj)
hdu = cls._readfrom_internal(fileobj, checksum=checksum,
ignore_missing_end=ignore_missing_end,
> **kwargs)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/base.py:379:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.hdu.base._BaseHDU'>
data = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/042f15bfd69d3d3153427aeb62d52f8f', mode 'rb' at 0x1042b5420>>
header = None, checksum = False, ignore_missing_end = False, kwargs = {}, hdu_buffer = None, hdu_fileobj = None, header_offset = 0
from_file = True
@classmethod
def _readfrom_internal(cls, data, header=None, checksum=False,
ignore_missing_end=False, **kwargs):
"""
Provides the bulk of the internal implementation for readfrom and
fromstring.
For some special cases, supports using a header that was already
created, and just using the input data for the actual array data.
"""
hdu_buffer = None
hdu_fileobj = None
header_offset = 0
if isinstance(data, _File):
from_file = True
if header is None:
header_offset = data.tell()
> header = Header.fromfile(data, endcard=not ignore_missing_end)
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/hdu/base.py:439:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.header.Header'>
fileobj = <astropy.io.fits.file._File <open file u'/var/folders/sb/4qv5j4m90pz1rw7m70rj1.../astropy/download/042f15bfd69d3d3153427aeb62d52f8f', mode 'rb' at 0x1042b5420>>
sep = '', endcard = True, padding = True
@classmethod
def fromfile(cls, fileobj, sep='', endcard=True, padding=True):
"""
Similar to :meth:`Header.fromstring`, but reads the header string from
a given file-like object or filename.
Parameters
----------
fileobj : str, file-like
A filename or an open file-like object from which a FITS header is
to be read. For open file handles the file pointer must be at the
beginning of the header.
sep : str, optional
The string separating cards from each other, such as a newline. By
default there is no card separator (as is the case in a raw FITS
file).
endcard : bool, optional
If True (the default) the header must end with an END card in order
to be considered valid. If an END card is not found an
`~.exceptions.IOError` is raised.
padding : bool, optional
If True (the default) the header will be required to be padded out
to a multiple of 2880, the FITS header block size. Otherwise any
padding, or lack thereof, is ignored.
Returns
-------
header
A new `Header` instance.
"""
close_file = False
if isinstance(fileobj, string_types):
# Open in text mode by default to support newline handling; if a
# binary-mode file object is passed in, the user is on their own
# with respect to newline handling
fileobj = open(fileobj, 'r')
close_file = True
try:
is_binary = fileobj_is_binary(fileobj)
def block_iter(nbytes):
while True:
data = fileobj.read(nbytes)
if data:
yield data
else:
break
return cls._from_blocks(block_iter, is_binary, sep, endcard,
> padding)[1]
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/header.py:462:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.io.fits.header.Header'>, block_iter = <function block_iter at 0x1042e7140>, is_binary = True, sep = ''
endcard = True, padding = True
@classmethod
def _from_blocks(cls, block_iter, is_binary, sep, endcard, padding):
"""
The meat of `Header.fromfile`; in a separate method so that
`Header.fromfile` itself is just responsible for wrapping file
handling. Also used by `_BaseHDU.fromstring`.
``block_iter`` should be a callable which, given a block size n
(typically 2880 bytes as used by the FITS standard) returns an iterator
of byte strings of that block size.
``is_binary`` specifies whether the returned blocks are bytes or text
Returns both the entire header *string*, and the `Header` object
returned by Header.fromstring on that string.
"""
actual_block_size = _block_size(sep)
clen = Card.length + len(sep)
blocks = block_iter(actual_block_size)
# Read the first header block.
try:
block = next(blocks)
except StopIteration:
raise EOFError()
if not is_binary:
# TODO: There needs to be error handling at *this* level for
# non-ASCII characters; maybe at this stage decoding latin-1 might
# be safer
block = encode_ascii(block)
read_blocks = []
is_eof = False
end_found = False
# continue reading header blocks until END card or EOF is reached
while True:
# find the END card
end_found, block = cls._find_end_card(block, clen)
read_blocks.append(decode_ascii(block))
if end_found:
break
try:
block = next(blocks)
except StopIteration:
is_eof = True
break
if not block:
is_eof = True
break
if not is_binary:
block = encode_ascii(block)
if not end_found and is_eof and endcard:
# TODO: Pass this error to validation framework as an ERROR,
# rather than raising an exception
> raise IOError('Header missing END card.')
E IOError: Header missing END card.
/Users/deil/Library/Python/2.7/lib/python/site-packages/astropy-0.4rc3.dev9437-py2.7-macosx-10.9-x86_64.egg/astropy/io/fits/header.py:531: IOError
============================================ 3 failed, 9 passed, 1 xpassed in 10.18 seconds =============================================
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