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test_core.py
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test_core.py
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# Licensed under a 3-clause BSD style license - see PYFITS.rst
from __future__ import division, with_statement
import gzip
import bz2
import io
import mmap
import os
import warnings
import zipfile
import numpy as np
try:
import StringIO
HAVE_STRINGIO = True
except ImportError:
HAVE_STRINGIO = False
from ....io import fits
from ....tests.helper import pytest, raises, catch_warnings, ignore_warnings
from ....utils.exceptions import AstropyDeprecationWarning
from ....utils.data import get_pkg_data_filename
from . import FitsTestCase
from ..convenience import _getext
from ..diff import FITSDiff
from ..file import _File, GZIP_MAGIC
try:
import pathlib
except ImportError:
HAS_PATHLIB = False
else:
HAS_PATHLIB = True
class TestCore(FitsTestCase):
def test_with_statement(self):
with fits.open(self.data('ascii.fits')) as f:
pass
@raises(IOError)
def test_missing_file(self):
fits.open(self.temp('does-not-exist.fits'))
def test_naxisj_check(self):
hdulist = fits.open(self.data('o4sp040b0_raw.fits'))
hdulist[1].header['NAXIS3'] = 500
assert 'NAXIS3' in hdulist[1].header
hdulist.verify('silentfix')
assert 'NAXIS3' not in hdulist[1].header
def test_byteswap(self):
p = fits.PrimaryHDU()
l = fits.HDUList()
n = np.zeros(3, dtype='i2')
n[0] = 1
n[1] = 60000
n[2] = 2
c = fits.Column(name='foo', format='i2', bscale=1, bzero=32768,
array=n)
t = fits.BinTableHDU.from_columns([c])
l.append(p)
l.append(t)
l.writeto(self.temp('test.fits'), clobber=True)
with fits.open(self.temp('test.fits')) as p:
assert p[1].data[1]['foo'] == 60000.0
@pytest.mark.skipif('not HAS_PATHLIB')
def test_fits_file_path_object(self):
"""
Testing when fits file is passed as pathlib.Path object #4412.
"""
fpath = pathlib.Path(get_pkg_data_filename('data/tdim.fits'))
hdulist = fits.open(fpath)
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
hdulist2 = fits.open(self.data('tdim.fits'))
assert FITSDiff(hdulist2, hdulist).identical is True
def test_add_del_columns(self):
p = fits.ColDefs([])
p.add_col(fits.Column(name='FOO', format='3J'))
p.add_col(fits.Column(name='BAR', format='1I'))
assert p.names == ['FOO', 'BAR']
p.del_col('FOO')
assert p.names == ['BAR']
def test_add_del_columns2(self):
hdulist = fits.open(self.data('tb.fits'))
table = hdulist[1]
assert table.data.dtype.names == ('c1', 'c2', 'c3', 'c4')
assert table.columns.names == ['c1', 'c2', 'c3', 'c4']
table.columns.del_col(str('c1'))
assert table.data.dtype.names == ('c2', 'c3', 'c4')
assert table.columns.names == ['c2', 'c3', 'c4']
table.columns.del_col(str('c3'))
assert table.data.dtype.names == ('c2', 'c4')
assert table.columns.names == ['c2', 'c4']
table.columns.add_col(fits.Column(str('foo'), str('3J')))
assert table.data.dtype.names == ('c2', 'c4', 'foo')
assert table.columns.names == ['c2', 'c4', 'foo']
hdulist.writeto(self.temp('test.fits'), clobber=True)
with ignore_warnings():
# TODO: The warning raised by this test is actually indication of a
# bug and should *not* be ignored. But as it is a known issue we
# hide it for now. See
# https://github.com/spacetelescope/PyFITS/issues/44
with fits.open(self.temp('test.fits')) as hdulist:
table = hdulist[1]
assert table.data.dtype.names == ('c2', 'c4', 'foo')
assert table.columns.names == ['c2', 'c4', 'foo']
@ignore_warnings(AstropyDeprecationWarning)
def test_update_header_card(self):
"""A very basic test for the Header.update method--I'd like to add a
few more cases to this at some point.
"""
header = fits.Header()
comment = 'number of bits per data pixel'
header['BITPIX'] = (16, comment)
assert 'BITPIX' in header
assert header['BITPIX'] == 16
assert header.ascard['BITPIX'].comment == comment
# The new API doesn't support savecomment so leave this line here; at
# any rate good to have testing of the new API mixed with the old API
header.update('BITPIX', 32, savecomment=True)
# Make sure the value has been updated, but the comment was preserved
assert header['BITPIX'] == 32
assert header.ascard['BITPIX'].comment == comment
# The comment should still be preserved--savecomment only takes effect
# if a new comment is also specified
header['BITPIX'] = 16
assert header.ascard['BITPIX'].comment == comment
header.update('BITPIX', 16, 'foobarbaz', savecomment=True)
assert header.ascard['BITPIX'].comment == comment
@ignore_warnings(AstropyDeprecationWarning)
def test_set_card_value(self):
"""Similar to test_update_header_card(), but tests the the
`header['FOO'] = 'bar'` method of updating card values.
"""
header = fits.Header()
comment = 'number of bits per data pixel'
card = fits.Card.fromstring('BITPIX = 32 / %s' % comment)
header.ascard.append(card)
header['BITPIX'] = 32
assert 'BITPIX' in header
assert header['BITPIX'] == 32
assert header.ascard['BITPIX'].key == 'BITPIX'
assert header.ascard['BITPIX'].value == 32
assert header.ascard['BITPIX'].comment == comment
def test_uint(self):
hdulist_f = fits.open(self.data('o4sp040b0_raw.fits'), uint=False)
hdulist_i = fits.open(self.data('o4sp040b0_raw.fits'), uint=True)
assert hdulist_f[1].data.dtype == np.float32
assert hdulist_i[1].data.dtype == np.uint16
assert np.all(hdulist_f[1].data == hdulist_i[1].data)
@ignore_warnings(AstropyDeprecationWarning)
def test_fix_missing_card_append(self):
hdu = fits.ImageHDU()
errs = hdu.req_cards('TESTKW', None, None, 'foo', 'silentfix', [])
assert len(errs) == 1
assert 'TESTKW' in hdu.header
assert hdu.header['TESTKW'] == 'foo'
assert hdu.header.ascard[-1].key == 'TESTKW'
def test_fix_invalid_keyword_value(self):
hdu = fits.ImageHDU()
hdu.header['TESTKW'] = 'foo'
errs = hdu.req_cards('TESTKW', None,
lambda v: v == 'foo', 'foo', 'ignore', [])
assert len(errs) == 0
# Now try a test that will fail, and ensure that an error will be
# raised in 'exception' mode
errs = hdu.req_cards('TESTKW', None, lambda v: v == 'bar', 'bar',
'exception', [])
assert len(errs) == 1
assert errs[0][1] == "'TESTKW' card has invalid value 'foo'."
# See if fixing will work
hdu.req_cards('TESTKW', None, lambda v: v == 'bar', 'bar', 'silentfix',
[])
assert hdu.header['TESTKW'] == 'bar'
@raises(fits.VerifyError)
def test_unfixable_missing_card(self):
class TestHDU(fits.hdu.base.NonstandardExtHDU):
def _verify(self, option='warn'):
errs = super(TestHDU, self)._verify(option)
hdu.req_cards('TESTKW', None, None, None, 'fix', errs)
return errs
@classmethod
def match_header(cls, header):
# Since creating this HDU class adds it to the registry we
# don't want the file reader to possibly think any actual
# HDU from a file should be handled by this class
return False
hdu = TestHDU(header=fits.Header())
hdu.verify('fix')
@raises(fits.VerifyError)
def test_exception_on_verification_error(self):
hdu = fits.ImageHDU()
del hdu.header['XTENSION']
hdu.verify('exception')
def test_ignore_verification_error(self):
hdu = fits.ImageHDU()
# The default here would be to issue a warning; ensure that no warnings
# or exceptions are raised
with catch_warnings():
warnings.simplefilter('error')
del hdu.header['NAXIS']
try:
hdu.verify('ignore')
except Exception as e:
self.fail('An exception occurred when the verification error '
'should have been ignored: %s' % exc)
# Make sure the error wasn't fixed either, silently or otherwise
assert 'NAXIS' not in hdu.header
@raises(ValueError)
def test_unrecognized_verify_option(self):
hdu = fits.ImageHDU()
hdu.verify('foobarbaz')
def test_combined_verify_options(self):
"""
Test verify options like fix+ignore.
"""
def make_invalid_hdu():
hdu = fits.ImageHDU()
# Add one keyword to the header that contains a fixable defect, and one
# with an unfixable defect
c1 = fits.Card.fromstring("test = ' test'")
c2 = fits.Card.fromstring("P.I. = ' Hubble'")
hdu.header.append(c1)
hdu.header.append(c2)
return hdu
# silentfix+ignore should be completely silent
hdu = make_invalid_hdu()
with catch_warnings():
warnings.simplefilter('error')
try:
hdu.verify('silentfix+ignore')
except Exception as exc:
self.fail('An exception occurred when the verification error '
'should have been ignored: %s' % exc)
# silentfix+warn should be quiet about the fixed HDU and only warn
# about the unfixable one
hdu = make_invalid_hdu()
with catch_warnings() as w:
hdu.verify('silentfix+warn')
assert len(w) == 4
assert 'Illegal keyword name' in str(w[2].message)
# silentfix+exception should only mention the unfixable error in the
# exception
hdu = make_invalid_hdu()
try:
hdu.verify('silentfix+exception')
except fits.VerifyError as exc:
assert 'Illegal keyword name' in str(exc)
assert 'not upper case' not in str(exc)
else:
self.fail('An exception should have been raised.')
# fix+ignore is not too useful, but it should warn about the fixed
# problems while saying nothing about the unfixable problems
hdu = make_invalid_hdu()
with catch_warnings() as w:
hdu.verify('fix+ignore')
assert len(w) == 4
assert 'not upper case' in str(w[2].message)
# fix+warn
hdu = make_invalid_hdu()
with catch_warnings() as w:
hdu.verify('fix+warn')
assert len(w) == 6
assert 'not upper case' in str(w[2].message)
assert 'Illegal keyword name' in str(w[4].message)
# fix+exception
hdu = make_invalid_hdu()
try:
hdu.verify('fix+exception')
except fits.VerifyError as exc:
assert 'Illegal keyword name' in str(exc)
assert 'not upper case' in str(exc)
else:
self.fail('An exception should have been raised.')
def test_getext(self):
"""
Test the various different ways of specifying an extension header in
the convenience functions.
"""
hl, ext = _getext(self.data('test0.fits'), 'readonly', 1)
assert ext == 1
pytest.raises(ValueError, _getext, self.data('test0.fits'), 'readonly',
1, 2)
pytest.raises(ValueError, _getext, self.data('test0.fits'), 'readonly',
(1, 2))
pytest.raises(ValueError, _getext, self.data('test0.fits'), 'readonly',
'sci', 'sci')
pytest.raises(TypeError, _getext, self.data('test0.fits'), 'readonly',
1, 2, 3)
hl, ext = _getext(self.data('test0.fits'), 'readonly', ext=1)
assert ext == 1
hl, ext = _getext(self.data('test0.fits'), 'readonly', ext=('sci', 2))
assert ext == ('sci', 2)
pytest.raises(TypeError, _getext, self.data('test0.fits'), 'readonly',
1, ext=('sci', 2), extver=3)
pytest.raises(TypeError, _getext, self.data('test0.fits'), 'readonly',
ext=('sci', 2), extver=3)
hl, ext = _getext(self.data('test0.fits'), 'readonly', 'sci')
assert ext == ('sci', 1)
hl, ext = _getext(self.data('test0.fits'), 'readonly', 'sci', 1)
assert ext == ('sci', 1)
hl, ext = _getext(self.data('test0.fits'), 'readonly', ('sci', 1))
assert ext == ('sci', 1)
hl, ext = _getext(self.data('test0.fits'), 'readonly', 'sci',
extver=1, do_not_scale_image_data=True)
assert ext == ('sci', 1)
pytest.raises(TypeError, _getext, self.data('test0.fits'), 'readonly',
'sci', ext=1)
pytest.raises(TypeError, _getext, self.data('test0.fits'), 'readonly',
'sci', 1, extver=2)
hl, ext = _getext(self.data('test0.fits'), 'readonly', extname='sci')
assert ext == ('sci', 1)
hl, ext = _getext(self.data('test0.fits'), 'readonly', extname='sci',
extver=1)
assert ext == ('sci', 1)
pytest.raises(TypeError, _getext, self.data('test0.fits'), 'readonly',
extver=1)
def test_extension_name_case_sensitive(self):
"""
Tests that setting fits.conf.extension_name_case_sensitive at
runtime works.
"""
if 'PYFITS_EXTENSION_NAME_CASE_SENSITIVE' in os.environ:
del os.environ['PYFITS_EXTENSION_NAME_CASE_SENSITIVE']
hdu = fits.ImageHDU()
hdu.name = 'sCi'
assert hdu.name == 'SCI'
assert hdu.header['EXTNAME'] == 'SCI'
with fits.conf.set_temp('extension_name_case_sensitive', True):
hdu = fits.ImageHDU()
hdu.name = 'sCi'
assert hdu.name == 'sCi'
assert hdu.header['EXTNAME'] == 'sCi'
hdu.name = 'sCi'
assert hdu.name == 'SCI'
assert hdu.header['EXTNAME'] == 'SCI'
def test_hdu_fromstring(self):
"""
Tests creating a fully-formed HDU object from a string containing the
bytes of the HDU.
"""
dat = open(self.data('test0.fits'), 'rb').read()
offset = 0
with fits.open(self.data('test0.fits')) as hdul:
hdulen = hdul[0]._data_offset + hdul[0]._data_size
hdu = fits.PrimaryHDU.fromstring(dat[:hdulen])
assert isinstance(hdu, fits.PrimaryHDU)
assert hdul[0].header == hdu.header
assert hdu.data is None
hdu.header['TEST'] = 'TEST'
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdul:
assert isinstance(hdu, fits.PrimaryHDU)
assert hdul[0].header[:-1] == hdu.header[:-1]
assert hdul[0].header['TEST'] == 'TEST'
assert hdu.data is None
with fits.open(self.data('test0.fits'))as hdul:
for ext_hdu in hdul[1:]:
offset += hdulen
hdulen = len(str(ext_hdu.header)) + ext_hdu._data_size
hdu = fits.ImageHDU.fromstring(dat[offset:offset + hdulen])
assert isinstance(hdu, fits.ImageHDU)
assert ext_hdu.header == hdu.header
assert (ext_hdu.data == hdu.data).all()
def test_nonstandard_hdu(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/157
Tests that "Nonstandard" HDUs with SIMPLE = F are read and written
without prepending a superfluous and unwanted standard primary HDU.
"""
data = np.arange(100, dtype=np.uint8)
hdu = fits.PrimaryHDU(data=data)
hdu.header['SIMPLE'] = False
hdu.writeto(self.temp('test.fits'))
info = [(0, '', 'NonstandardHDU', 5, (), '', '')]
with fits.open(self.temp('test.fits')) as hdul:
assert hdul.info(output=False) == info
# NonstandardHDUs just treat the data as an unspecified array of
# bytes. The first 100 bytes should match the original data we
# passed in...the rest should be zeros padding out the rest of the
# FITS block
assert (hdul[0].data[:100] == data).all()
assert (hdul[0].data[100:] == 0).all()
def test_extname(self):
"""Test getting/setting the EXTNAME of an HDU."""
h1 = fits.PrimaryHDU()
assert h1.name == 'PRIMARY'
# Normally a PRIMARY HDU should not have an EXTNAME, though it should
# have a default .name attribute
assert 'EXTNAME' not in h1.header
# The current version of the FITS standard does allow PRIMARY HDUs to
# have an EXTNAME, however.
h1.name = 'NOTREAL'
assert h1.name == 'NOTREAL'
assert h1.header.get('EXTNAME') == 'NOTREAL'
# Updating the EXTNAME in the header should update the .name
h1.header['EXTNAME'] = 'TOOREAL'
assert h1.name == 'TOOREAL'
# If we delete an EXTNAME keyword from a PRIMARY HDU it should go back
# to the default
del h1.header['EXTNAME']
assert h1.name == 'PRIMARY'
# For extension HDUs the situation is a bit simpler:
h2 = fits.ImageHDU()
assert h2.name == ''
assert 'EXTNAME' not in h2.header
h2.name = 'HELLO'
assert h2.name == 'HELLO'
assert h2.header.get('EXTNAME') == 'HELLO'
h2.header['EXTNAME'] = 'GOODBYE'
assert h2.name == 'GOODBYE'
def test_extver_extlevel(self):
"""Test getting/setting the EXTVER and EXTLEVEL of and HDU."""
# EXTVER and EXTNAME work exactly the same; their semantics are, for
# now, to be inferred by the user. Although they should never be less
# than 1, the standard does not explicitly forbid any value so long as
# it's an integer
h1 = fits.PrimaryHDU()
assert h1.ver == 1
assert h1.level == 1
assert 'EXTVER' not in h1.header
assert 'EXTLEVEL' not in h1.header
h1.ver = 2
assert h1.header.get('EXTVER') == 2
h1.header['EXTVER'] = 3
assert h1.ver == 3
del h1.header['EXTVER']
h1.ver == 1
h1.level = 2
assert h1.header.get('EXTLEVEL') == 2
h1.header['EXTLEVEL'] = 3
assert h1.level == 3
del h1.header['EXTLEVEL']
assert h1.level == 1
pytest.raises(TypeError, setattr, h1, 'ver', 'FOO')
pytest.raises(TypeError, setattr, h1, 'level', 'BAR')
def test_consecutive_writeto(self):
"""
Regression test for an issue where calling writeto twice on the same
HDUList could write a corrupted file.
https://github.com/spacetelescope/PyFITS/issues/40 is actually a
particular instance of this problem, though isn't unique to sys.stdout.
"""
with fits.open(self.data('test0.fits')) as hdul1:
# Add a bunch of header keywords so that the data will be forced to
# new offsets within the file:
for idx in range(40):
hdul1[1].header['TEST%d' % idx] = 'test'
hdul1.writeto(self.temp('test1.fits'))
hdul1.writeto(self.temp('test2.fits'))
# Open a second handle to the original file and compare it to hdul1
# (We only compare part of the one header that was modified)
# Compare also with the second writeto output
with fits.open(self.data('test0.fits')) as hdul2:
with fits.open(self.temp('test2.fits')) as hdul3:
for hdul in (hdul1, hdul3):
for idx, hdus in enumerate(zip(hdul1, hdul)):
hdu1, hdu2 = hdus
if idx != 1:
assert hdu1.header == hdu2.header
else:
assert (hdu1.header ==
hdu2.header[:len(hdu1.header)])
assert np.all(hdu1.data == hdu2.data)
class TestConvenienceFunctions(FitsTestCase):
def test_writeto(self):
"""
Simple test for writing a trivial header and some data to a file
with the `writeto()` convenience function.
"""
data = np.zeros((100, 100))
header = fits.Header()
fits.writeto(self.temp('array.fits'), data, header=header,
clobber=True)
hdul = fits.open(self.temp('array.fits'))
assert len(hdul) == 1
assert (data == hdul[0].data).all()
@ignore_warnings(AstropyDeprecationWarning)
def test_writeto_2(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/107
Test of `writeto()` with a trivial header containing a single keyword.
"""
data = np.zeros((100,100))
header = fits.Header()
header.set('CRPIX1', 1.)
fits.writeto(self.temp('array.fits'), data, header=header,
clobber=True, output_verify='silentfix')
hdul = fits.open(self.temp('array.fits'))
assert len(hdul) == 1
assert (data == hdul[0].data).all()
assert 'CRPIX1' in hdul[0].header
assert hdul[0].header['CRPIX1'] == 1.0
class TestFileFunctions(FitsTestCase):
"""
Tests various basic I/O operations, specifically in the
astropy.io.fits.file._File class.
"""
def test_open_nonexistent(self):
"""Test that trying to open a non-existent file results in an
IOError (and not some other arbitrary exception).
"""
try:
fits.open(self.temp('foobar.fits'))
except IOError as e:
assert 'No such file or directory' in str(e)
except:
raise
# But opening in ostream or append mode should be okay, since they
# allow writing new files
for mode in ('ostream', 'append'):
with fits.open(self.temp('foobar.fits'), mode=mode) as h:
pass
assert os.path.exists(self.temp('foobar.fits'))
os.remove(self.temp('foobar.fits'))
def test_open_gzipped(self):
with ignore_warnings():
assert len(fits.open(self._make_gzip_file())) == 5
def test_detect_gzipped(self):
"""Test detection of a gzip file when the extension is not .gz."""
with ignore_warnings():
assert len(fits.open(self._make_gzip_file('test0.fz'))) == 5
def test_writeto_append_mode_gzip(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/33
Check that a new GzipFile opened in append mode can be used to write
out a new FITS file.
"""
# Note: when opening a GzipFile the 'b+' is superfluous, but this was
# still how the original test case looked
# Note: with statement not supported on GzipFile in older Python
# versions
fileobj = gzip.GzipFile(self.temp('test.fits.gz'), 'ab+')
h = fits.PrimaryHDU()
try:
h.writeto(fileobj)
finally:
fileobj.close()
with fits.open(self.temp('test.fits.gz')) as hdul:
assert hdul[0].header == h.header
def test_open_bzipped(self):
with ignore_warnings():
assert len(fits.open(self._make_bzip2_file())) == 5
def test_detect_bzipped(self):
"""Test detection of a bzip2 file when the extension is not .bz2."""
with ignore_warnings():
assert len(fits.open(self._make_bzip2_file('test0.xx'))) == 5
def test_writeto_bzip2_fileobj(self):
"""Test writing to a bz2.BZ2File file like object"""
fileobj = bz2.BZ2File(self.temp('test.fits.bz2'), 'w')
h = fits.PrimaryHDU()
try:
h.writeto(fileobj)
finally:
fileobj.close()
with fits.open(self.temp('test.fits.bz2')) as hdul:
assert hdul[0].header == h.header
def test_writeto_bzip2_filename(self):
"""Test writing to a bzip2 file by name"""
filename = self.temp('testname.fits.bz2')
h = fits.PrimaryHDU()
h.writeto(filename)
with fits.open(self.temp('testname.fits.bz2')) as hdul:
assert hdul[0].header == h.header
def test_open_zipped(self):
zf = self._make_zip_file()
with ignore_warnings():
assert len(fits.open(self._make_zip_file())) == 5
with ignore_warnings():
assert len(fits.open(zipfile.ZipFile(zf))) == 5
def test_detect_zipped(self):
"""Test detection of a zip file when the extension is not .zip."""
zf = self._make_zip_file(filename='test0.fz')
with ignore_warnings():
assert len(fits.open(zf)) == 5
def test_open_zipped_writeable(self):
"""Opening zipped files in a writeable mode should fail."""
zf = self._make_zip_file()
pytest.raises(IOError, fits.open, zf, 'update')
pytest.raises(IOError, fits.open, zf, 'append')
zf = zipfile.ZipFile(zf, 'a')
pytest.raises(IOError, fits.open, zf, 'update')
pytest.raises(IOError, fits.open, zf, 'append')
def test_read_open_astropy_gzip_file(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2774
This tests reading from a ``GzipFile`` object from Astropy's
compatibility copy of the ``gzip`` module.
"""
gf = gzip.GzipFile(self._make_gzip_file())
try:
assert len(fits.open(gf)) == 5
finally:
gf.close()
@raises(IOError)
def test_open_multiple_member_zipfile(self):
"""
Opening zip files containing more than one member files should fail
as there's no obvious way to specify which file is the FITS file to
read.
"""
zfile = zipfile.ZipFile(self.temp('test0.zip'), 'w')
zfile.write(self.data('test0.fits'))
zfile.writestr('foo', 'bar')
zfile.close()
fits.open(zfile.filename)
def test_read_open_file(self):
"""Read from an existing file object."""
with open(self.data('test0.fits'), 'rb') as f:
assert len(fits.open(f)) == 5
def test_read_closed_file(self):
"""Read from an existing file object that's been closed."""
f = open(self.data('test0.fits'), 'rb')
f.close()
assert len(fits.open(f)) == 5
def test_read_open_gzip_file(self):
"""Read from an open gzip file object."""
gf = gzip.GzipFile(self._make_gzip_file())
try:
assert len(fits.open(gf)) == 5
finally:
gf.close()
def test_open_gzip_file_for_writing(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/195."""
gf = self._make_gzip_file()
with fits.open(gf, mode='update') as h:
h[0].header['EXPFLAG'] = 'ABNORMAL'
with fits.open(gf) as h:
# Just to make sur ethe update worked; if updates work
# normal writes should work too...
assert h[0].header['EXPFLAG'] == 'ABNORMAL'
def test_write_read_gzip_file(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2794
Ensure files written through gzip are readable.
"""
data = np.arange(100)
hdu = fits.PrimaryHDU(data=data)
hdu.writeto(self.temp('test.fits.gz'))
with open(self.temp('test.fits.gz'), 'rb') as f:
assert f.read(3) == GZIP_MAGIC
with fits.open(self.temp('test.fits.gz')) as hdul:
assert np.all(hdul[0].data == data)
def test_read_file_like_object(self):
"""Test reading a FITS file from a file-like object."""
filelike = io.BytesIO()
with open(self.data('test0.fits'), 'rb') as f:
filelike.write(f.read())
filelike.seek(0)
with ignore_warnings():
assert len(fits.open(filelike)) == 5
def test_updated_file_permissions(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/79
Tests that when a FITS file is modified in update mode, the file
permissions are preserved.
"""
filename = self.temp('test.fits')
hdul = [fits.PrimaryHDU(), fits.ImageHDU()]
hdul = fits.HDUList(hdul)
hdul.writeto(filename)
old_mode = os.stat(filename).st_mode
hdul = fits.open(filename, mode='update')
hdul.insert(1, fits.ImageHDU())
hdul.flush()
hdul.close()
assert old_mode == os.stat(filename).st_mode
def test_fileobj_mode_guessing(self):
"""Tests whether a file opened without a specified pyfits mode
('readonly', etc.) is opened in a mode appropriate for the given file
object.
"""
self.copy_file('test0.fits')
# Opening in text mode should outright fail
for mode in ('r', 'w', 'a'):
with open(self.temp('test0.fits'), mode) as f:
pytest.raises(ValueError, fits.HDUList.fromfile, f)
# Need to re-copy the file since opening it in 'w' mode blew it away
self.copy_file('test0.fits')
with open(self.temp('test0.fits'), 'rb') as f:
with fits.HDUList.fromfile(f) as h:
assert h.fileinfo(0)['filemode'] == 'readonly'
for mode in ('wb', 'ab'):
with open(self.temp('test0.fits'), mode) as f:
with fits.HDUList.fromfile(f) as h:
# Basically opening empty files for output streaming
assert len(h) == 0
# Need to re-copy the file since opening it in 'w' mode blew it away
self.copy_file('test0.fits')
with open(self.temp('test0.fits'), 'wb+') as f:
with fits.HDUList.fromfile(f) as h:
# wb+ still causes an existing file to be overwritten so there
# are no HDUs
assert len(h) == 0
# Need to re-copy the file since opening it in 'w' mode blew it away
self.copy_file('test0.fits')
with open(self.temp('test0.fits'), 'rb+') as f:
with fits.HDUList.fromfile(f) as h:
assert h.fileinfo(0)['filemode'] == 'update'
with open(self.temp('test0.fits'), 'ab+') as f:
with fits.HDUList.fromfile(f) as h:
assert h.fileinfo(0)['filemode'] == 'append'
def test_mmap_unwriteable(self):
"""Regression test for https://github.com/astropy/astropy/issues/968
Temporarily patches mmap.mmap to exhibit platform-specific bad
behavior.
"""
class MockMmap(mmap.mmap):
def flush(self):
raise mmap.error('flush is broken on this platform')
old_mmap = mmap.mmap
mmap.mmap = MockMmap
# Force the mmap test to be rerun
_File.__dict__['_mmap_available']._cache.clear()
try:
self.copy_file('test0.fits')
with catch_warnings() as w:
with fits.open(self.temp('test0.fits'), mode='update',
memmap=True) as h:
h[1].data[0, 0] = 999
assert len(w) == 1
assert 'mmap.flush is unavailable' in str(w[0].message)
# Double check that writing without mmap still worked
with fits.open(self.temp('test0.fits')) as h:
assert h[1].data[0, 0] == 999
finally:
mmap.mmap = old_mmap
_File.__dict__['_mmap_available']._cache.clear()
def test_mmap_closing(self):
"""
Tests that the mmap reference is closed/removed when there aren't any
HDU data references left.
"""
if not _File._mmap_available:
pytest.xfail('not expected to work on platforms without mmap '
'support')
with fits.open(self.data('test0.fits'), memmap=True) as hdul:
assert hdul._file._mmap is None
hdul[1].data
assert hdul._file._mmap is not None
del hdul[1].data
# Should be no more references to data in the file so close the
# mmap
assert hdul._file._mmap is None
hdul[1].data
hdul[2].data
del hdul[1].data
# hdul[2].data is still references so keep the mmap open
assert hdul._file._mmap is not None
del hdul[2].data
assert hdul._file._mmap is None
assert hdul._file._mmap is None
with fits.open(self.data('test0.fits'), memmap=True) as hdul:
hdul[1].data
# When the only reference to the data is on the hdu object, and the
# hdulist it belongs to has been closed, the mmap should be closed as
# well
assert hdul._file._mmap is None
with fits.open(self.data('test0.fits'), memmap=True) as hdul:
data = hdul[1].data
# also make a copy
data_copy = data.copy()
# The HDUList is closed; in fact, get rid of it completely
del hdul
# The data array should still work though...
assert np.all(data == data_copy)
def test_uncloseable_file(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2356
Demonstrates that FITS files can still be read from "file-like" objects
that don't have an obvious "open" or "closed" state.
"""
class MyFileLike(object):
def __init__(self, foobar):
self._foobar = foobar
def read(self, n):
return self._foobar.read(n)
def seek(self, offset, whence=os.SEEK_SET):
self._foobar.seek(offset, whence)
def tell(self):
return self._foobar.tell()
with open(self.data('test0.fits'), 'rb') as f:
fileobj = MyFileLike(f)
with fits.open(fileobj) as hdul1:
with fits.open(self.data('test0.fits')) as hdul2:
assert hdul1.info(output=False) == hdul2.info(output=False)
for hdu1, hdu2 in zip(hdul1, hdul2):
assert hdu1.header == hdu2.header
if hdu1.data is not None and hdu2.data is not None:
assert np.all(hdu1.data == hdu2.data)
@pytest.mark.skipif('not HAVE_STRINGIO')
def test_write_stringio(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2463
Only test against `StringIO.StringIO` on Python versions that have it.
Note: `io.StringIO` is not supported for this purpose as it does not
accept a bytes stream.
"""
self._test_write_string_bytes_io(StringIO.StringIO())
@pytest.mark.skipif('not HAVE_STRINGIO')
def test_write_stringio_discontiguous(self):
"""
Regression test related to
https://github.com/astropy/astropy/issues/2794#issuecomment-55441539
Demonstrates that writing an HDU containing a discontiguous Numpy array
should work properly.
"""
data = np.arange(100)[::3]
hdu = fits.PrimaryHDU(data=data)
fileobj = StringIO.StringIO()
hdu.writeto(fileobj)