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astrofrog/astropy_pypy.log

Created December 18, 2019 11:13
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astropy_pypy.log
============================= test session starts ==============================
platform linux -- Python 3.6.9[pypy-7.2.0-final], pytest-5.3.2, py-1.8.0, pluggy-0.13.1
Running tests with Astropy version 4.0.
Running tests in pypy/site-packages/astropy.
Date: 2019-12-18T11:05:26
Platform: Linux-5.3.0-24-generic-x86_64-with-debian-buster-sid
Executable: /home/tom/pypy/bin/pypy
Full Python Version:
3.6.9 (5da45ced70e515f94686be0df47c59abd1348ebc, Oct 17 2019, 22:59:56)
[PyPy 7.2.0 with GCC 8.2.0]
encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15
Package versions:
Numpy: 1.17.4
Scipy: not available
Matplotlib: not available
h5py: not available
Pandas: not available
Cython: not available
Scikit-image: not available
asdf: not available
astropy-helpers: 4.0
Using Astropy options: remote_data: none.
rootdir: /home/tom
plugins: hypothesis-4.55.2, remotedata-0.3.2, openfiles-0.4.0, doctestplus-0.5.0, astropy-header-0.1.1, arraydiff-0.3
collected 13614 items / 26 skipped / 13588 selected
pypy/site-packages/astropy/_erfa/tests/test_erfa.py .................... [ 0%]
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pypy/site-packages/astropy/config/tests/test_configs.py ................ [ 0%]
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pypy/site-packages/astropy/constants/tests/test_constant.py ........ [ 0%]
pypy/site-packages/astropy/constants/tests/test_pickle.py ......... [ 0%]
pypy/site-packages/astropy/constants/tests/test_prior_version.py ....... [ 0%]
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pypy/site-packages/astropy/constants/tests/test_sciencestate.py .. [ 0%]
pypy/site-packages/astropy/convolution/tests/test_convolve.py .......... [ 0%]
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pypy/site-packages/astropy/coordinates/tests/test_angles.py ............ [ 10%]
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pypy/site-packages/astropy/coordinates/tests/test_angular_separation.py . [ 10%]
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pypy/site-packages/astropy/coordinates/tests/test_arrays.py ............ [ 10%]
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pypy/site-packages/astropy/coordinates/tests/test_atc_replacements.py .. [ 10%]
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pypy/site-packages/astropy/coordinates/tests/test_celestial_transformations.py . [ 10%]
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pypy/site-packages/astropy/coordinates/tests/test_matrix_utilities.py .. [ 12%]
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pypy/site-packages/astropy/coordinates/tests/test_representation_methods.py . [ 14%]
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pypy/site-packages/astropy/coordinates/tests/test_sites.py .ss.s... [ 14%]
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pypy/site-packages/astropy/coordinates/tests/test_sky_coord_velocities.py . [ 17%]
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pypy/site-packages/astropy/coordinates/tests/test_skyoffset_transformations.py . [ 18%]
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pypy/site-packages/astropy/coordinates/tests/test_solar_system.py s....s [ 18%]
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pypy/site-packages/astropy/coordinates/tests/test_transformations.py ... [ 18%]
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pypy/site-packages/astropy/coordinates/tests/test_velocity_corrs.py ssss [ 18%]
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pypy/site-packages/astropy/coordinates/tests/accuracy/test_fk4_no_e_fk5.py . [ 18%]
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pypy/site-packages/astropy/coordinates/tests/accuracy/test_galactic_fk4.py . [ 18%]
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pypy/site-packages/astropy/coordinates/tests/accuracy/test_icrs_fk5.py . [ 18%]
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pypy/site-packages/astropy/cosmology/tests/test_cosmology.py ..sss..s.ss [ 19%]
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pypy/site-packages/astropy/cosmology/tests/test_pickle.py ... [ 19%]
pypy/site-packages/astropy/io/ascii/tests/test_c_reader.py ............. [ 19%]
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pypy/site-packages/astropy/io/ascii/tests/test_cds_header_from_readme.py . [ 20%]
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pypy/site-packages/astropy/io/ascii/tests/test_write.py ................ [ 22%]
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pypy/site-packages/astropy/io/fits/tests/test_checksum.py FFFFFFFFFFFF.F [ 23%]
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pypy/site-packages/astropy/io/fits/tests/test_convenience.py F.......... [ 24%]
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pypy/site-packages/astropy/io/fits/tests/test_header.py ................ [ 26%]
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pypy/site-packages/astropy/io/fits/tests/test_image.py ......FF.F..FFFFF [ 27%]
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pypy/site-packages/astropy/io/fits/tests/test_nonstandard.py FFF [ 28%]
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pypy/site-packages/astropy/io/fits/tests/test_table.py .FFFFFFFFFFF.F.FF [ 28%]
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pypy/site-packages/astropy/io/fits/tests/test_uint.py FFFFFFFFF [ 28%]
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pypy/site-packages/astropy/io/misc/tests/test_pickle_helpers.py .... [ 29%]
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pypy/site-packages/astropy/io/tests/test_registry.py ................... [ 29%]
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pypy/site-packages/astropy/io/tests/test_registry_help.py ......... [ 30%]
pypy/site-packages/astropy/io/votable/tests/converter_test.py .......... [ 30%]
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pypy/site-packages/astropy/io/votable/tests/exception_test.py .. [ 30%]
pypy/site-packages/astropy/io/votable/tests/resource_test.py . [ 30%]
pypy/site-packages/astropy/io/votable/tests/table_test.py .............. [ 30%]
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pypy/site-packages/astropy/io/votable/tests/tree_test.py ... [ 30%]
pypy/site-packages/astropy/io/votable/tests/ucd_test.py ..... [ 30%]
pypy/site-packages/astropy/io/votable/tests/util_test.py ........... [ 30%]
pypy/site-packages/astropy/io/votable/tests/vo_test.py ................. [ 30%]
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pypy/site-packages/astropy/modeling/tests/test_functional_models.py .... [ 32%]
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pypy/site-packages/astropy/modeling/tests/test_input.py ...............s [ 33%]
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pypy/site-packages/astropy/modeling/tests/test_mappings.py ......s.. [ 33%]
pypy/site-packages/astropy/modeling/tests/test_math_func.py . [ 33%]
pypy/site-packages/astropy/modeling/tests/test_model_sets.py ........ [ 33%]
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pypy/site-packages/astropy/modeling/tests/test_physical_models.py .....s [ 36%]
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pypy/site-packages/astropy/modeling/tests/test_polynomial.py sssssssssss [ 36%]
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pypy/site-packages/astropy/modeling/tests/test_projections.py .......... [ 37%]
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pypy/site-packages/astropy/modeling/tests/test_quantities_evaluation.py . [ 38%]
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pypy/site-packages/astropy/modeling/tests/test_quantities_fitting.py sss [ 38%]
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pypy/site-packages/astropy/modeling/tests/test_quantities_parameters.py . [ 39%]
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pypy/site-packages/astropy/nddata/tests/test_bitmask.py ................ [ 41%]
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=================================== FAILURES ===================================
____________________ TestChecksumFunctions.test_sample_file ____________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000ff9dfa0>
def test_sample_file(self):
hdul = fits.open(self.data('checksum.fits'), checksum=True)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:41:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestChecksumFunctions.test_image_create ____________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000e1ce988>
def test_image_create(self):
n = np.arange(100, dtype=np.int64)
hdu = fits.PrimaryHDU(n)
hdu.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert (hdu.data == hdul[0].data).all()
assert 'CHECKSUM' in hdul[0].header
assert 'DATASUM' in hdul[0].header
if not sys.platform.startswith('win32'):
# The checksum ends up being different on Windows, possibly due
# to slight floating point differences
assert hdul[0].header['CHECKSUM'] == 'ZHMkeGKjZGKjbGKj'
> assert hdul[0].header['DATASUM'] == '4950'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:56:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestChecksumFunctions.test_scaled_data ____________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000001d1cd408>
def test_scaled_data(self):
with fits.open(self.data('scale.fits')) as hdul:
orig_data = hdul[0].data.copy()
hdul[0].scale('int16', 'old')
hdul.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul1:
assert (hdul1[0].data == orig_data).all()
assert 'CHECKSUM' in hdul1[0].header
assert hdul1[0].header['CHECKSUM'] == 'cUmaeUjZcUjacUjW'
assert 'DATASUM' in hdul1[0].header
> assert hdul1[0].header['DATASUM'] == '1891563534'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001d1cde88>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001d1cde88>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000001d1cd408>
def test_scaled_data(self):
with fits.open(self.data('scale.fits')) as hdul:
orig_data = hdul[0].data.copy()
hdul[0].scale('int16', 'old')
hdul.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul1:
assert (hdul1[0].data == orig_data).all()
assert 'CHECKSUM' in hdul1[0].header
assert hdul1[0].header['CHECKSUM'] == 'cUmaeUjZcUjacUjW'
assert 'DATASUM' in hdul1[0].header
> assert hdul1[0].header['DATASUM'] == '1891563534'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestChecksumFunctions.test_scaled_data_auto_rescale ______________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x0000000011571e50>
def test_scaled_data_auto_rescale(self):
"""
Regression test for
https://github.com/astropy/astropy/issues/3883#issuecomment-115122647
Ensure that when scaled data is automatically rescaled on
opening/writing a file that the checksum and datasum are computed for
the rescaled array.
"""
with fits.open(self.data('scale.fits')) as hdul:
# Write out a copy of the data with the rescaling applied
> hdul.writeto(self.temp('rescaled.fits'))
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:82:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestChecksumFunctions.test_uint16_data ____________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x00000000150a0528>
def test_uint16_data(self):
checksums = [
('aDcXaCcXaCcXaCcX', '0'), ('oYiGqXi9oXiEoXi9', '1746888714'),
('VhqQWZoQVfoQVZoQ', '0'), ('4cPp5aOn4aOn4aOn', '0'),
('8aCN8X9N8aAN8W9N', '1756785133'), ('UhqdUZnbUfnbUZnb', '0'),
('4cQJ5aN94aNG4aN9', '0')]
with fits.open(self.data('o4sp040b0_raw.fits'), uint=True) as hdul:
hdul.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), uint=True,
checksum=True) as hdul1:
for idx, (hdu_a, hdu_b) in enumerate(zip(hdul, hdul1)):
if hdu_a.data is None or hdu_b.data is None:
assert hdu_a.data is hdu_b.data
else:
assert (hdu_a.data == hdu_b.data).all()
assert 'CHECKSUM' in hdul[idx].header
assert hdul[idx].header['CHECKSUM'] == checksums[idx][0]
assert 'DATASUM' in hdul[idx].header
> assert hdul[idx].header['DATASUM'] == checksums[idx][1]
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:130:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000e4e8170>, <astropy.io.fits.hdu.image.ImageHDU object at 0x...ts.hdu.image.ImageHDU object at 0x0000000013ac2c28>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000014e667c8>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000e4e8170>, <astropy.io.fits.hdu.image.ImageHDU object at 0x...ts.hdu.image.ImageHDU object at 0x0000000013ac2c28>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000014e667c8>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x00000000150a0528>
def test_uint16_data(self):
checksums = [
('aDcXaCcXaCcXaCcX', '0'), ('oYiGqXi9oXiEoXi9', '1746888714'),
('VhqQWZoQVfoQVZoQ', '0'), ('4cPp5aOn4aOn4aOn', '0'),
('8aCN8X9N8aAN8W9N', '1756785133'), ('UhqdUZnbUfnbUZnb', '0'),
('4cQJ5aN94aNG4aN9', '0')]
with fits.open(self.data('o4sp040b0_raw.fits'), uint=True) as hdul:
hdul.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), uint=True,
checksum=True) as hdul1:
for idx, (hdu_a, hdu_b) in enumerate(zip(hdul, hdul1)):
if hdu_a.data is None or hdu_b.data is None:
assert hdu_a.data is hdu_b.data
else:
assert (hdu_a.data == hdu_b.data).all()
assert 'CHECKSUM' in hdul[idx].header
assert hdul[idx].header['CHECKSUM'] == checksums[idx][0]
assert 'DATASUM' in hdul[idx].header
> assert hdul[idx].header['DATASUM'] == checksums[idx][1]
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:130:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestChecksumFunctions.test_groups_hdu_data __________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000f115830>
def test_groups_hdu_data(self):
imdata = np.arange(100.0)
imdata.shape = (10, 1, 1, 2, 5)
pdata1 = np.arange(10) + 0.1
pdata2 = 42
x = fits.hdu.groups.GroupData(imdata, parnames=['abc', 'xyz'],
pardata=[pdata1, pdata2], bitpix=-32)
hdu = fits.GroupsHDU(x)
hdu.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert comparerecords(hdul[0].data, hdu.data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == '3eDQAZDO4dDOAZDO'
assert 'DATASUM' in hdul[0].header
> assert hdul[0].header['DATASUM'] == '2797758084'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:146:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestChecksumFunctions.test_binary_table_data _________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000d29df30>
def test_binary_table_data(self):
a1 = np.array(['NGC1001', 'NGC1002', 'NGC1003'])
a2 = np.array([11.1, 12.3, 15.2])
col1 = fits.Column(name='target', format='20A', array=a1)
col2 = fits.Column(name='V_mag', format='E', array=a2)
cols = fits.ColDefs([col1, col2])
tbhdu = fits.BinTableHDU.from_columns(cols)
tbhdu.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert comparerecords(tbhdu.data, hdul[1].data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in hdul[1].header
assert hdul[1].header['CHECKSUM'] == 'aD1Oa90MaC0Ma90M'
assert 'DATASUM' in hdul[1].header
> assert hdul[1].header['DATASUM'] == '1062205743'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:165:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestChecksumFunctions.test_variable_length_table_data _____________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x0000000016b18e20>
def test_variable_length_table_data(self):
c1 = fits.Column(name='var', format='PJ()',
array=np.array([[45.0, 56], np.array([11, 12, 13])],
'O'))
c2 = fits.Column(name='xyz', format='2I', array=[[11, 3], [12, 4]])
tbhdu = fits.BinTableHDU.from_columns([c1, c2])
tbhdu.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert comparerecords(tbhdu.data, hdul[1].data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in hdul[1].header
assert hdul[1].header['CHECKSUM'] == 'YIGoaIEmZIEmaIEm'
assert 'DATASUM' in hdul[1].header
> assert hdul[1].header['DATASUM'] == '1507485'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:183:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestChecksumFunctions.test_ascii_table_data __________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000001107fad0>
def test_ascii_table_data(self):
a1 = np.array(['abc', 'def'])
r1 = np.array([11.0, 12.0])
c1 = fits.Column(name='abc', format='A3', array=a1)
# This column used to be E format, but the single-precision float lost
# too much precision when scaling so it was changed to a D
c2 = fits.Column(name='def', format='D', array=r1, bscale=2.3,
bzero=0.6)
c3 = fits.Column(name='t1', format='I', array=[91, 92, 93])
x = fits.ColDefs([c1, c2, c3])
hdu = fits.TableHDU.from_columns(x)
hdu.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert comparerecords(hdu.data, hdul[1].data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
if not sys.platform.startswith('win32'):
# The checksum ends up being different on Windows, possibly due
# to slight floating point differences
assert 'CHECKSUM' in hdul[1].header
assert hdul[1].header['CHECKSUM'] == '3rKFAoI94oICAoI9'
assert 'DATASUM' in hdul[1].header
> assert hdul[1].header['DATASUM'] == '1914653725'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:210:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestChecksumFunctions.test_compressed_image_data _______________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000d32cb48>
def test_compressed_image_data(self):
with fits.open(self.data('comp.fits')) as h1:
h1.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as h2:
assert np.all(h1[1].data == h2[1].data)
assert 'CHECKSUM' in h2[0].header
assert h2[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in h2[0].header
assert h2[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in h2[1].header
assert h2[1].header['CHECKSUM'] == 'ZeAbdb8aZbAabb7a'
assert 'DATASUM' in h2[1].header
> assert h2[1].header['DATASUM'] == '113055149'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:224:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001692e090>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000017f452f0>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001692e090>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000017f452f0>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000d32cb48>
def test_compressed_image_data(self):
with fits.open(self.data('comp.fits')) as h1:
h1.writeto(self.temp('tmp.fits'), overwrite=True, checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as h2:
assert np.all(h1[1].data == h2[1].data)
assert 'CHECKSUM' in h2[0].header
assert h2[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in h2[0].header
assert h2[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in h2[1].header
assert h2[1].header['CHECKSUM'] == 'ZeAbdb8aZbAabb7a'
assert 'DATASUM' in h2[1].header
> assert h2[1].header['DATASUM'] == '113055149'
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:224:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestChecksumFunctions.test_compressed_image_data_int16 ____________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000c664608>
def test_compressed_image_data_int16(self):
n = np.arange(100, dtype='int16')
hdu = fits.ImageHDU(n)
comp_hdu = fits.CompImageHDU(hdu.data, hdu.header)
comp_hdu.writeto(self.temp('tmp.fits'), checksum=True)
hdu.writeto(self.temp('uncomp.fits'), checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert np.all(hdul[1].data == comp_hdu.data)
assert np.all(hdul[1].data == hdu.data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in hdul[1].header
assert hdul[1]._header['CHECKSUM'] == 'J5cCJ5c9J5cAJ5c9'
assert 'DATASUM' in hdul[1].header
assert hdul[1]._header['DATASUM'] == '2453673070'
assert 'CHECKSUM' in hdul[1].header
with fits.open(self.temp('uncomp.fits'), checksum=True) as hdul2:
header_comp = hdul[1]._header
header_uncomp = hdul2[1].header
assert 'ZHECKSUM' in header_comp
assert 'CHECKSUM' in header_uncomp
assert header_uncomp['CHECKSUM'] == 'ZE94eE91ZE91bE91'
assert header_comp['ZHECKSUM'] == header_uncomp['CHECKSUM']
assert 'ZDATASUM' in header_comp
assert 'DATASUM' in header_uncomp
assert header_uncomp['DATASUM'] == '160565700'
> assert header_comp['ZDATASUM'] == header_uncomp['DATASUM']
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:256:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000ee83520>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000e027750>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000ee83520>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000e027750>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000c664608>
def test_compressed_image_data_int16(self):
n = np.arange(100, dtype='int16')
hdu = fits.ImageHDU(n)
comp_hdu = fits.CompImageHDU(hdu.data, hdu.header)
comp_hdu.writeto(self.temp('tmp.fits'), checksum=True)
hdu.writeto(self.temp('uncomp.fits'), checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert np.all(hdul[1].data == comp_hdu.data)
assert np.all(hdul[1].data == hdu.data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in hdul[1].header
assert hdul[1]._header['CHECKSUM'] == 'J5cCJ5c9J5cAJ5c9'
assert 'DATASUM' in hdul[1].header
assert hdul[1]._header['DATASUM'] == '2453673070'
assert 'CHECKSUM' in hdul[1].header
with fits.open(self.temp('uncomp.fits'), checksum=True) as hdul2:
header_comp = hdul[1]._header
header_uncomp = hdul2[1].header
assert 'ZHECKSUM' in header_comp
assert 'CHECKSUM' in header_uncomp
assert header_uncomp['CHECKSUM'] == 'ZE94eE91ZE91bE91'
assert header_comp['ZHECKSUM'] == header_uncomp['CHECKSUM']
assert 'ZDATASUM' in header_comp
assert 'DATASUM' in header_uncomp
assert header_uncomp['DATASUM'] == '160565700'
> assert header_comp['ZDATASUM'] == header_uncomp['DATASUM']
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:256:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________ TestChecksumFunctions.test_compressed_image_data_float32 ___________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000d2ea288>
def test_compressed_image_data_float32(self):
n = np.arange(100, dtype='float32')
hdu = fits.ImageHDU(n)
comp_hdu = fits.CompImageHDU(hdu.data, hdu.header)
comp_hdu.writeto(self.temp('tmp.fits'), checksum=True)
hdu.writeto(self.temp('uncomp.fits'), checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert np.all(hdul[1].data == comp_hdu.data)
assert np.all(hdul[1].data == hdu.data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in hdul[1].header
assert 'DATASUM' in hdul[1].header
if not sys.platform.startswith('win32'):
# The checksum ends up being different on Windows, possibly due
# to slight floating point differences
assert hdul[1]._header['CHECKSUM'] == 'eATIf3SHe9SHe9SH'
assert hdul[1]._header['DATASUM'] == '1277667818'
with fits.open(self.temp('uncomp.fits'), checksum=True) as hdul2:
header_comp = hdul[1]._header
header_uncomp = hdul2[1].header
assert 'ZHECKSUM' in header_comp
assert 'CHECKSUM' in header_uncomp
assert header_uncomp['CHECKSUM'] == 'Cgr5FZo2Cdo2CZo2'
assert header_comp['ZHECKSUM'] == header_uncomp['CHECKSUM']
assert 'ZDATASUM' in header_comp
assert 'DATASUM' in header_uncomp
assert header_uncomp['DATASUM'] == '2393636889'
> assert header_comp['ZDATASUM'] == header_uncomp['DATASUM']
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:291:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000e10e448>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000e10e6b0>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000e10e448>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000e10e6b0>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000d2ea288>
def test_compressed_image_data_float32(self):
n = np.arange(100, dtype='float32')
hdu = fits.ImageHDU(n)
comp_hdu = fits.CompImageHDU(hdu.data, hdu.header)
comp_hdu.writeto(self.temp('tmp.fits'), checksum=True)
hdu.writeto(self.temp('uncomp.fits'), checksum=True)
with fits.open(self.temp('tmp.fits'), checksum=True) as hdul:
assert np.all(hdul[1].data == comp_hdu.data)
assert np.all(hdul[1].data == hdu.data)
assert 'CHECKSUM' in hdul[0].header
assert hdul[0].header['CHECKSUM'] == 'D8iBD6ZAD6fAD6ZA'
assert 'DATASUM' in hdul[0].header
assert hdul[0].header['DATASUM'] == '0'
assert 'CHECKSUM' in hdul[1].header
assert 'DATASUM' in hdul[1].header
if not sys.platform.startswith('win32'):
# The checksum ends up being different on Windows, possibly due
# to slight floating point differences
assert hdul[1]._header['CHECKSUM'] == 'eATIf3SHe9SHe9SH'
assert hdul[1]._header['DATASUM'] == '1277667818'
with fits.open(self.temp('uncomp.fits'), checksum=True) as hdul2:
header_comp = hdul[1]._header
header_uncomp = hdul2[1].header
assert 'ZHECKSUM' in header_comp
assert 'CHECKSUM' in header_uncomp
assert header_uncomp['CHECKSUM'] == 'Cgr5FZo2Cdo2CZo2'
assert header_comp['ZHECKSUM'] == header_uncomp['CHECKSUM']
assert 'ZDATASUM' in header_comp
assert 'DATASUM' in header_uncomp
assert header_uncomp['DATASUM'] == '2393636889'
> assert header_comp['ZDATASUM'] == header_uncomp['DATASUM']
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:291:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestChecksumFunctions.test_append _______________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000ef70a30>
def test_append(self):
hdul = fits.open(self.data('tb.fits'))
hdul.writeto(self.temp('tmp.fits'), overwrite=True)
n = np.arange(100)
fits.append(self.temp('tmp.fits'), n, checksum=True)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:302:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestChecksumFunctions.test_writeto_convenience ________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x00000000041d75c8>
def test_writeto_convenience(self):
n = np.arange(100)
fits.writeto(self.temp('tmp.fits'), n, overwrite=True, checksum=True)
hdul = fits.open(self.temp('tmp.fits'), checksum=True)
self._check_checksums(hdul[0])
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:312:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestChecksumFunctions.test_hdu_writeto_existing ________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000c63a100>
def test_hdu_writeto_existing(self):
"""
Tests that when using writeto with checksum=True, a checksum and
datasum are added to HDUs that did not previously have one.
Regression test for https://github.com/spacetelescope/PyFITS/issues/8
"""
with fits.open(self.data('tb.fits')) as hdul:
> hdul.writeto(self.temp('test.fits'), checksum=True)
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:331:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________ TestChecksumFunctions.test_open_update_mode_preserve_checksum _________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000000c4eef00>
def test_open_update_mode_preserve_checksum(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/148 where
checksums are being removed from headers when a file is opened in
update mode, even though no changes were made to the file.
"""
self.copy_file('checksum.fits')
with fits.open(self.temp('checksum.fits')) as hdul:
> data = hdul[1].data.copy()
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:365:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestChecksumFunctions.test_open_update_mode_update_checksum __________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x000000002082a170>
def test_open_update_mode_update_checksum(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/148, part
2. This ensures that if a file contains a checksum, the checksum is
updated when changes are saved to the file, even if the file was opened
with the default of checksum=False.
An existing checksum and/or datasum are only stripped if the file is
opened with checksum='remove'.
"""
self.copy_file('checksum.fits')
with fits.open(self.temp('checksum.fits')) as hdul:
header = hdul[1].header.copy()
> data = hdul[1].data.copy()
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:389:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestChecksumFunctions.test_overwrite_invalid _________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x0000000013adfbe8>
def test_overwrite_invalid(self):
"""
Tests that invalid checksum or datasum are overwriten when the file is
saved.
"""
reffile = self.temp('ref.fits')
with fits.open(self.data('tb.fits')) as hdul:
> hdul.writeto(reffile, checksum=True)
pypy/site-packages/astropy/io/fits/tests/test_checksum.py:427:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________________ TestSingleTable.test_memmap __________________________
self = <astropy.io.fits.tests.test_connect.TestSingleTable object at 0x000000000da78aa0>
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_memmap0')
def test_memmap(self, tmpdir):
filename = str(tmpdir.join('test_simple.fts'))
t1 = Table(self.data)
t1.write(filename, overwrite=True)
t2 = Table.read(filename, memmap=False)
> t3 = Table.read(filename, memmap=True)
pypy/site-packages/astropy/io/fits/tests/test_connect.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/table/connect.py:52: in __call__
out = registry.read(cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/io/fits/connect.py:218: in read_table_fits
hdulist.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestSingleTable.test_character_as_bytes[True] _________________
self = <astropy.io.fits.tests.test_connect.TestSingleTable object at 0x000000001699c090>
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_character_as_bytes_True_0')
memmap = True
@pytest.mark.parametrize('memmap', (False, True))
def test_character_as_bytes(self, tmpdir, memmap):
filename = str(tmpdir.join('test_simple.fts'))
t1 = Table(self.data)
t1.write(filename, overwrite=True)
> t2 = Table.read(filename, character_as_bytes=False, memmap=memmap)
pypy/site-packages/astropy/io/fits/tests/test_connect.py:253:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/table/connect.py:52: in __call__
out = registry.read(cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/io/fits/connect.py:218: in read_table_fits
hdulist.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________________ test_bool_column _______________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_bool_column0')
def test_bool_column(tmpdir):
"""
Regression test for https://github.com/astropy/astropy/issues/1953
Ensures that Table columns of bools are properly written to a FITS table.
"""
arr = np.ones(5, dtype=bool)
arr[::2] == np.False_
t = Table([arr])
t.write(str(tmpdir.join('test.fits')), overwrite=True)
with fits.open(str(tmpdir.join('test.fits'))) as hdul:
assert hdul[1].data['col0'].dtype == np.dtype('bool')
> assert np.all(hdul[1].data['col0'] == arr)
pypy/site-packages/astropy/io/fits/tests/test_connect.py:541:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________________ test_unicode_column ______________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_unicode_column0')
def test_unicode_column(tmpdir):
"""
Test that a column of unicode strings is still written as one
byte-per-character in the FITS table (so long as the column can be ASCII
encoded).
Regression test for one of the issues fixed in
https://github.com/astropy/astropy/pull/4228
"""
t = Table([np.array(['a', 'b', 'cd'])])
t.write(str(tmpdir.join('test.fits')), overwrite=True)
with fits.open(str(tmpdir.join('test.fits'))) as hdul:
assert np.all(hdul[1].data['col0'] == ['a', 'b', 'cd'])
> assert hdul[1].header['TFORM1'] == '2A'
pypy/site-packages/astropy/io/fits/tests/test_connect.py:559:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestConvenience.test_resource_warning _____________________
self = <astropy.io.fits.tests.test_convenience.TestConvenience object at 0x000000000fbfcd78>
def test_resource_warning(self):
warnings.simplefilter('always', ResourceWarning)
with catch_warnings() as w:
> _ = fits.getdata(self.data('test0.fits'))
pypy/site-packages/astropy/io/fits/tests/test_convenience.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestConvenience.test_image_extension_update_header ______________
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002061a4f0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000002061a528>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
> self.flush(output_verify=output_verify, verbose=verbose)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:963:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = ([<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002061a4f0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000002061a528>],)
kwargs = {'output_verify': 'exception', 'verbose': False}
curr_thread = <_MainThread(MainThread, started 140018066300352)>
single_thread = True
SigintHandler = <class 'astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler'>
sigint_handler = <astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler object at 0x000000002061be88>
old_handler = <built-in function default_int_handler>
@wraps(func)
def wrapped(*args, **kwargs):
# Get the name of the current thread and determine if this is a single
# threaded application
curr_thread = threading.currentThread()
single_thread = (threading.activeCount() == 1 and
curr_thread.getName() == 'MainThread')
class SigintHandler:
def __init__(self):
self.sigint_received = False
def __call__(self, signum, frame):
warnings.warn('KeyboardInterrupt ignored until {} is '
'complete!'.format(func.__name__),
AstropyUserWarning)
self.sigint_received = True
sigint_handler = SigintHandler()
# Define new signal interput handler
if single_thread:
# Install new handler
old_handler = signal.signal(signal.SIGINT, sigint_handler)
try:
> func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/util.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002061a4f0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000002061a528>]
output_verify = 'exception', verbose = False
@ignore_sigint
def flush(self, output_verify='fix', verbose=False):
"""
Force a write of the `HDUList` back to the file (for append and
update modes only).
Parameters
----------
output_verify : str
Output verification option. Must be one of ``"fix"``,
``"silentfix"``, ``"ignore"``, ``"warn"``, or
``"exception"``. May also be any combination of ``"fix"`` or
``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception"
(e.g. ``"fix+warn"``). See :ref:`verify` for more info.
verbose : bool
When `True`, print verbose messages
"""
if self._file.mode not in ('append', 'update', 'ostream'):
warnings.warn("Flush for '{}' mode is not supported."
.format(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 {} to {}.'.format(
filename, backup), AstropyUserWarning)
try:
shutil.copy(filename, backup)
except OSError as exc:
raise OSError('Failed to save backup to destination {}: '
'{}'.format(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)
with _free_space_check(self):
hdu._writeto(self._file)
if verbose:
print('append HDU', hdu.name, extver)
hdu._new = False
hdu._postwriteto()
elif self._file.mode == 'update':
> self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002061a4f0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000002061a528>]
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002061a4f0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000002061a528>]
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+')
elif self._file.compression == 'bzip2':
if not HAS_BZ2:
raise ModuleNotFoundError(
"This Python installation does not provide the bz2 module.")
new_file = bz2.BZ2File(name, mode='w')
else:
new_file = name
with self.fromfile(new_file, mode='append') as hdulist:
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1307:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_convenience.TestConvenience object at 0x000000002061b4b0>
def test_image_extension_update_header(self):
"""
Test that _makehdu correctly includes the header. For example in the
fits.update convenience function.
"""
filename = self.temp('twoextension.fits')
hdus = [fits.PrimaryHDU(np.zeros((10, 10))),
fits.ImageHDU(np.zeros((10, 10)))]
fits.HDUList(hdus).writeto(filename)
fits.update(filename,
np.zeros((10, 10)),
header=fits.Header([('WHAT', 100)]),
> ext=1)
pypy/site-packages/astropy/io/fits/tests/test_convenience.py:192:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:723: in update
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestConvenience.test_printdiff ________________________
self = <astropy.io.fits.tests.test_convenience.TestConvenience object at 0x0000000018cf09c0>
def test_printdiff(self):
"""
Test that FITSDiff can run the different inputs without crashing.
"""
# Testing different string input options
> assert printdiff(self.data('arange.fits'),
self.data('blank.fits')) is None
pypy/site-packages/astropy/io/fits/tests/test_convenience.py:202:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:871: in printdiff
print(FITSDiff(inputa, inputb, **kwargs).report())
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestConvenience.test_tabledump ________________________
self = <astropy.io.fits.tests.test_convenience.TestConvenience object at 0x0000000018893d38>
def test_tabledump(self):
"""
Regression test for https://github.com/astropy/astropy/issues/6937
"""
# copy fits file to the temp directory
self.copy_file('tb.fits')
# test without datafile
> fits.tabledump(self.temp('tb.fits'))
pypy/site-packages/astropy/io/fits/tests/test_convenience.py:237:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/utils/decorators.py:521: in wrapper
return function(*args, **kwargs)
pypy/site-packages/astropy/io/fits/convenience.py:937: in tabledump
f.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestConvenience.test_append_filename _____________________
self = <astropy.io.fits.tests.test_convenience.TestConvenience object at 0x000000001ba47210>
def test_append_filename(self):
"""
Test fits.append with a filename argument.
"""
data = np.arange(6)
testfile = self.temp('test_append_1.fits')
# Test case 1: creation of file
fits.append(testfile, data=data, checksum=True)
# Test case 2: append to existing file, with verify=True
# Also test that additional keyword can be passed to fitsopen
fits.append(testfile, data=data * 2, checksum=True, ignore_blank=True)
# Test case 3: append to existing file, with verify=False
fits.append(testfile, data=data * 3, checksum=True, verify=False)
with fits.open(testfile, checksum=True) as hdu1:
np.testing.assert_array_equal(hdu1[0].data, data)
np.testing.assert_array_equal(hdu1[1].data, data * 2)
> np.testing.assert_array_equal(hdu1[2].data, data * 3)
pypy/site-packages/astropy/io/fits/tests/test_convenience.py:264:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestConvenience.test_append_with_header ____________________
self = <astropy.io.fits.tests.test_convenience.TestConvenience object at 0x000000001126ae90>
def test_append_with_header(self):
"""
Test fits.append with a fits Header, which triggers detection of the
HDU class. Regression test for
https://github.com/astropy/astropy/issues/8660
"""
testfile = self.temp('test_append_1.fits')
with fits.open(self.data('test0.fits')) as hdus:
for hdu in hdus:
> fits.append(testfile, hdu.data, hdu.header, checksum=True)
pypy/site-packages/astropy/io/fits/tests/test_convenience.py:284:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________________ TestCore.test_byteswap ____________________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x000000000c9e9ad0>
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'), overwrite=True)
with fits.open(self.temp('test.fits')) as p:
> assert p[1].data[1]['foo'] == 60000.0
pypy/site-packages/astropy/io/fits/tests/test_core.py:74:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestCore.test_fits_file_path_object ______________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x00000000169591d8>
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'))
with fits.open(fpath) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data('tdim.fits')) as hdulist2:
> assert FITSDiff(hdulist2, hdulist).identical is True
pypy/site-packages/astropy/io/fits/tests/test_core.py:86:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x00000000169597f8>, <astropy.io.fits.hdu.table.BinTableHDU object at 0x0000000016958cd0>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x00000000169597f8>, <astropy.io.fits.hdu.table.BinTableHDU object at 0x0000000016958cd0>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_core.TestCore object at 0x00000000169591d8>
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'))
with fits.open(fpath) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data('tdim.fits')) as hdulist2:
> assert FITSDiff(hdulist2, hdulist).identical is True
pypy/site-packages/astropy/io/fits/tests/test_core.py:86:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestCore.test_add_del_columns2 ________________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x000000000dd6d0f8>
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('c1')
pypy/site-packages/astropy/io/fits/tests/test_core.py:101:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/column.py:1743: in del_col
self._notify('column_removed', self, indx)
pypy/site-packages/astropy/io/fits/util.py:137: in _notify
method(*args, **kwargs)
pypy/site-packages/astropy/io/fits/hdu/table.py:589: in _update_column_removed
super()._update_column_removed(columns, idx)
pypy/site-packages/astropy/io/fits/hdu/table.py:233: in _update_column_removed
del self.data
pypy/site-packages/astropy/utils/decorators.py:765: in __delete__
self.fdel(obj)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.table.BinTableHDU object at 0x000000000dd6c090>
def data(self):
# The deleter
if self._file is not None and self._data_loaded:
> data_refcount = sys.getrefcount(self.data)
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/hdu/base.py:117: AttributeError
______________________________ TestCore.test_uint ______________________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x00000000152f48e0>
def test_uint(self):
filename = self.data('o4sp040b0_raw.fits')
with fits.open(filename, uint=False) as hdulist_f:
with fits.open(filename, uint=True) as hdulist_i:
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)
pypy/site-packages/astropy/io/fits/tests/test_core.py:164:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001533c3a0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000001533c3d8>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001533c3a0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000001533c3d8>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_core.TestCore object at 0x00000000152f48e0>
def test_uint(self):
filename = self.data('o4sp040b0_raw.fits')
with fits.open(filename, uint=False) as hdulist_f:
with fits.open(filename, uint=True) as hdulist_i:
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)
pypy/site-packages/astropy/io/fits/tests/test_core.py:164:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________________ TestCore.test_hdu_fromstring _________________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x00000000161efc20>
def test_hdu_fromstring(self):
"""
Tests creating a fully-formed HDU object from a string containing the
bytes of the HDU.
"""
infile = self.data('test0.fits')
outfile = self.temp('test.fits')
with open(infile, 'rb') as fin:
dat = fin.read()
offset = 0
with fits.open(infile) 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(outfile)
with fits.open(outfile) 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(infile)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()
pypy/site-packages/astropy/io/fits/tests/test_core.py:431:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestCore.test_nonstandard_hdu _________________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x00000000185c5210>
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, '', 1, '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()
pypy/site-packages/astropy/io/fits/tests/test_core.py:454:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestCore.test_consecutive_writeto _______________________
self = <astropy.io.fits.tests.test_core.TestCore object at 0x0000000004e7a9c0>
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[f'TEST{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(hdul2, hdul)):
hdu2, hdu = hdus
if idx != 1:
assert hdu.header == hdu2.header
else:
assert (hdu2.header ==
hdu.header[:len(hdu2.header)])
> assert np.all(hdu.data == hdu2.data)
pypy/site-packages/astropy/io/fits/tests/test_core.py:551:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x00000000064b07c8>, <astropy.io.fits.hdu.image.ImageHDU object at 0x...ts.hdu.image.ImageHDU object at 0x000000001f919a60>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000001f85be18>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x00000000064b07c8>, <astropy.io.fits.hdu.image.ImageHDU object at 0x...ts.hdu.image.ImageHDU object at 0x000000001f919a60>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000001f85be18>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_core.TestCore object at 0x0000000004e7a9c0>
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[f'TEST{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(hdul2, hdul)):
hdu2, hdu = hdus
if idx != 1:
assert hdu.header == hdu2.header
else:
assert (hdu2.header ==
hdu.header[:len(hdu2.header)])
> assert np.all(hdu.data == hdu2.data)
pypy/site-packages/astropy/io/fits/tests/test_core.py:551:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001456c790>, <astropy.io.fits.hdu.image.ImageHDU object at 0x...ts.hdu.image.ImageHDU object at 0x000000000e414db0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000e414de8>]
type = <class 'AttributeError'>
value = AttributeError("module 'sys' has no attribute 'getrefcount'",)
traceback = <traceback object at 0x0000000014c6a040>
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001456c790>, <astropy.io.fits.hdu.image.ImageHDU object at 0x...ts.hdu.image.ImageHDU object at 0x000000000e414db0>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000e414de8>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_core.TestCore object at 0x0000000004e7a9c0>
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[f'TEST{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(hdul2, hdul)):
hdu2, hdu = hdus
if idx != 1:
assert hdu.header == hdu2.header
else:
assert (hdu2.header ==
hdu.header[:len(hdu2.header)])
> assert np.all(hdu.data == hdu2.data)
pypy/site-packages/astropy/io/fits/tests/test_core.py:551:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestConvenienceFunctions.test_writeto _____________________
self = <astropy.io.fits.tests.test_core.TestConvenienceFunctions object at 0x000000000dd445d0>
def test_writeto(self):
"""
Simple test for writing a trivial header and some data to a file
with the `writeto()` convenience function.
"""
filename = self.temp('array.fits')
data = np.zeros((100, 100))
header = fits.Header()
fits.writeto(filename, data, header=header, overwrite=True)
with fits.open(filename) as hdul:
assert len(hdul) == 1
> assert (data == hdul[0].data).all()
pypy/site-packages/astropy/io/fits/tests/test_core.py:566:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestConvenienceFunctions.test_writeto_2 ____________________
self = <astropy.io.fits.tests.test_core.TestConvenienceFunctions object at 0x000000000b64a090>
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.
"""
filename = self.temp('array.fits')
data = np.zeros((100, 100))
header = fits.Header()
header.set('CRPIX1', 1.)
fits.writeto(filename, data, header=header,
overwrite=True, output_verify='silentfix')
with fits.open(filename) as hdul:
assert len(hdul) == 1
assert (data == hdul[0].data).all()
assert 'CRPIX1' in hdul[0].header
> assert hdul[0].header['CRPIX1'] == 1.0
pypy/site-packages/astropy/io/fits/tests/test_core.py:584:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestFileFunctions.test_updated_file_permissions ________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x000000000cca3088>
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()
pypy/site-packages/astropy/io/fits/tests/test_core.py:947:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/util.py:241: in wrapped
func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842: in flush
self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258: in _flush_update
self._flush_resize()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1307: in _flush_resize
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestFileFunctions.test_mmap_unwriteable ____________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x0000000016b18f70>
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 OSError('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
pypy/site-packages/astropy/io/fits/tests/test_core.py:1027:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestFileFunctions.test_mmap_allocate_error __________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x000000001831dbb0>
@pytest.mark.openfiles_ignore
def test_mmap_allocate_error(self):
"""
Regression test for https://github.com/astropy/astropy/issues/1380
Temporarily patches mmap.mmap to raise an OSError if mode is ACCESS_COPY.
"""
mmap_original = mmap.mmap
# We patch mmap here to raise an error if access=mmap.ACCESS_COPY, which
# emulates an issue that an OSError is raised if the available address
# space is less than the size of the file even if memory mapping is used.
def mmap_patched(*args, **kwargs):
if kwargs.get('access') == mmap.ACCESS_COPY:
exc = OSError()
exc.errno = errno.ENOMEM
raise exc
else:
return mmap_original(*args, **kwargs)
with fits.open(self.data('test0.fits'), memmap=True) as hdulist:
with patch.object(mmap, 'mmap', side_effect=mmap_patched) as p:
with pytest.warns(AstropyUserWarning, match=r"Could not memory "
r"map array with mode='readonly'"):
data = hdulist[1].data
p.reset_mock()
> assert not data.flags.writeable
pypy/site-packages/astropy/io/fits/tests/test_core.py:1060:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestFileFunctions.test_mmap_closing ______________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x0000000015357f30>
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
pypy/site-packages/astropy/io/fits/tests/test_core.py:1078:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.utils.decorators.lazyproperty object at 0x00007f587adbe7a0>
obj = <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000018b3d4b0>
def __delete__(self, obj):
if self.fdel:
> self.fdel(obj)
pypy/site-packages/astropy/utils/decorators.py:765:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000018b3d4b0>
def data(self):
# The deleter
if self._file is not None and self._data_loaded:
> data_refcount = sys.getrefcount(self.data)
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/hdu/base.py:117: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x0000000015357f30>
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
pypy/site-packages/astropy/io/fits/tests/test_core.py:1089:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestFileFunctions.test_uncloseable_file ____________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x0000000017a7a8e0>
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:
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)
pypy/site-packages/astropy/io/fits/tests/test_core.py:1142:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestFileFunctions.test_write_bytesio _____________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x00000000153a1910>
def test_write_bytesio(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2463
Test againt `io.BytesIO`. `io.StringIO` is not supported.
"""
> self._test_write_string_bytes_io(io.BytesIO())
pypy/site-packages/astropy/io/fits/tests/test_core.py:1170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_core.py:1254: in _test_write_string_bytes_io
assert FITSDiff(hdul, hdul2).identical
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestFileFunctions.test_filename_with_colon __________________
self = <astropy.io.fits.tests.test_core.TestFileFunctions object at 0x000000001484cfa8>
@pytest.mark.skipif('sys.platform.startswith("win32")')
def test_filename_with_colon(self):
"""
Test reading and writing a file with a colon in the filename.
Regression test for https://github.com/astropy/astropy/issues/3122
"""
# Skip on Windows since colons in filenames makes NTFS sad.
filename = 'APEXHET.2014-04-01T15:18:01.000.fits'
hdu = fits.PrimaryHDU(data=np.arange(10))
hdu.writeto(self.temp(filename))
with fits.open(self.temp(filename)) as hdul:
> assert np.all(hdul[0].data == hdu.data)
pypy/site-packages/astropy/io/fits/tests/test_core.py:1187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestStreamingFunctions.test_streaming_hdu_write_file _____________
self = <astropy.io.fits.tests.test_core.TestStreamingFunctions object at 0x000000000f204c60>
def test_streaming_hdu_write_file(self):
"""Test streaming an HDU to an open file object."""
arr = np.zeros((5, 5), dtype=np.int32)
with open(self.temp('new.fits'), 'ab+') as f:
shdu = self._make_streaming_hdu(f)
shdu.write(arr)
assert shdu.writecomplete
assert shdu.size == 100
with fits.open(self.temp('new.fits')) as hdul:
assert len(hdul) == 1
> assert (hdul[0].data == arr).all()
pypy/site-packages/astropy/io/fits/tests/test_core.py:1313:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestStreamingFunctions.test_blank_ignore ___________________
self = <astropy.io.fits.tests.test_core.TestStreamingFunctions object at 0x000000002213a5d0>
def test_blank_ignore(self):
with fits.open(self.data('blank.fits'), ignore_blank=True) as f:
> assert f[0].data.flat[0] == 2
pypy/site-packages/astropy/io/fits/tests/test_core.py:1372:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestStreamingFunctions.test_error_if_memmap_impossible ____________
self = <astropy.io.fits.tests.test_core.TestStreamingFunctions object at 0x0000000022906c60>
def test_error_if_memmap_impossible(self):
pth = self.data('blank.fits')
with fits.open(pth, memmap=True) as hdul:
with pytest.raises(ValueError):
> hdul[0].data
pypy/site-packages/astropy/io/fits/tests/test_core.py:1378:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestDiff.test_identical_comp_image_hdus ____________________
self = <astropy.io.fits.tests.test_diff.TestDiff object at 0x000000001fdc8bb8>
def test_identical_comp_image_hdus(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/189
For this test we mostly just care that comparing to compressed images
does not crash, and returns the correct results. Two compressed images
will be considered identical if the decompressed data is the same.
Obviously we test whether or not the same compression was used by
looking for (or ignoring) header differences.
"""
data = np.arange(100.0).reshape(10, 10)
hdu = fits.CompImageHDU(data=data)
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdula, \
fits.open(self.temp('test.fits')) as hdulb:
diff = FITSDiff(hdula, hdulb)
> assert diff.identical
pypy/site-packages/astropy/io/fits/tests/test_diff.py:335:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001feff558>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x000000001fefe758>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001feff558>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x000000001fefe758>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_diff.TestDiff object at 0x000000001fdc8bb8>
def test_identical_comp_image_hdus(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/189
For this test we mostly just care that comparing to compressed images
does not crash, and returns the correct results. Two compressed images
will be considered identical if the decompressed data is the same.
Obviously we test whether or not the same compression was used by
looking for (or ignoring) header differences.
"""
data = np.arange(100.0).reshape(10, 10)
hdu = fits.CompImageHDU(data=data)
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdula, \
fits.open(self.temp('test.fits')) as hdulb:
diff = FITSDiff(hdula, hdulb)
> assert diff.identical
pypy/site-packages/astropy/io/fits/tests/test_diff.py:335:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestDiff.test_identical_files_basic ______________________
self = <astropy.io.fits.tests.test_diff.TestDiff object at 0x000000000d5294e8>
def test_identical_files_basic(self):
"""Test identicality of two simple, extensionless files."""
a = np.arange(100).reshape(10, 10)
hdu = PrimaryHDU(data=a)
hdu.writeto(self.temp('testa.fits'))
hdu.writeto(self.temp('testb.fits'))
> diff = FITSDiff(self.temp('testa.fits'), self.temp('testb.fits'))
pypy/site-packages/astropy/io/fits/tests/test_diff.py:586:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestDivisionFunctions.test_rec_from_string __________________
self = <astropy.io.fits.tests.test_division.TestDivisionFunctions object at 0x000000000a477520>
def test_rec_from_string(self):
with fits.open(self.data('tb.fits')) as t1:
> s = t1[1].data.tostring()
pypy/site-packages/astropy/io/fits/tests/test_division.py:15:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestFitscheck.test_valid_file _________________________
self = <astropy.io.fits.tests.test_fitscheck.TestFitscheck object at 0x000000000cb4d948>
capsys = <_pytest.capture.CaptureFixture object at 0x000000000cb4c720>
def test_valid_file(self, capsys):
testfile = self.data('checksum.fits')
> assert fitscheck.main([testfile]) == 0
E AssertionError: assert 1 == 0
E + where 1 = <function main at 0x0000000008e0eb60>(['/home/tom/pypy/site-packages/astropy/io/fits/tests/data/checksum.fits'])
E + where <function main at 0x0000000008e0eb60> = fitscheck.main
pypy/site-packages/astropy/io/fits/tests/test_fitscheck.py:23: AssertionError
----------------------------- Captured stderr call -----------------------------
--- Logging error ---
Traceback (most recent call last):
File "/home/tom/pypy/site-packages/astropy/io/fits/scripts/fitscheck.py", line 190, in process_file
checksum_errors = verify_checksums(filename)
File "/home/tom/pypy/site-packages/astropy/io/fits/scripts/fitscheck.py", line 145, in verify_checksums
return 1
File "/home/tom/pypy/site-packages/astropy/io/fits/hdu/hdulist.py", line 381, in __exit__
self.close()
File "/home/tom/pypy/site-packages/astropy/io/fits/hdu/hdulist.py", line 966, in close
self._file.close()
File "/home/tom/pypy/site-packages/astropy/io/fits/file.py", line 413, in close
self._maybe_close_mmap()
File "/home/tom/pypy/site-packages/astropy/io/fits/file.py", line 431, in _maybe_close_mmap
sys.getrefcount(self._mmap) == 2 + refcount_delta):
AttributeError: module 'sys' has no attribute 'getrefcount'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/logging/__init__.py", line 996, in emit
stream.write(msg)
ValueError: I/O operation on closed file
Call stack:
File "<string>", line 1, in <module>
File "/home/tom/pypy/site-packages/astropy/tests/runner.py", line 266, in test
return runner.run_tests(**kwargs)
File "/home/tom/pypy/site-packages/astropy/tests/runner.py", line 611, in run_tests
return super().run_tests(**kwargs)
File "/home/tom/pypy/site-packages/astropy/tests/runner.py", line 248, in run_tests
return pytest.main(args=args, plugins=plugins)
File "/home/tom/pypy/site-packages/_pytest/config/__init__.py", line 92, in main
config=config
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/main.py", line 239, in pytest_cmdline_main
return wrap_session(config, _main)
File "/home/tom/pypy/site-packages/_pytest/main.py", line 196, in wrap_session
session.exitstatus = doit(config, session) or 0
File "/home/tom/pypy/site-packages/_pytest/main.py", line 246, in _main
config.hook.pytest_runtestloop(session=session)
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/main.py", line 270, in pytest_runtestloop
item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 81, in pytest_runtest_protocol
runtestprotocol(item, nextitem=nextitem)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 96, in runtestprotocol
reports.append(call_and_report(item, "call", log))
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 182, in call_and_report
call = call_runtest_hook(item, when, **kwds)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 207, in call_runtest_hook
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 234, in from_call
result = func()
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 207, in <lambda>
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 131, in pytest_runtest_call
item.runtest()
File "/home/tom/pypy/site-packages/_pytest/python.py", line 1435, in runtest
self.ihook.pytest_pyfunc_call(pyfuncitem=self)
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/python.py", line 166, in pytest_pyfunc_call
result = testfunction(**testargs)
File "/home/tom/pypy/site-packages/astropy/io/fits/tests/test_fitscheck.py", line 23, in test_valid_file
assert fitscheck.main([testfile]) == 0
File "/home/tom/pypy/site-packages/astropy/io/fits/scripts/fitscheck.py", line 213, in main
errors += process_file(filename)
File "/home/tom/pypy/site-packages/astropy/io/fits/scripts/fitscheck.py", line 199, in process_file
log.error(f'EXCEPTION {filename!r} .. {e}')
Message: "EXCEPTION '/home/tom/pypy/site-packages/astropy/io/fits/tests/data/checksum.fits' .. module 'sys' has no attribute 'getrefcount'"
Arguments: ()
EXCEPTION '/home/tom/pypy/site-packages/astropy/io/fits/tests/data/checksum.fits' .. module 'sys' has no attribute 'getrefcount'
--- Logging error ---
Traceback (most recent call last):
File "/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/logging/__init__.py", line 996, in emit
stream.write(msg)
ValueError: I/O operation on closed file
Call stack:
File "<string>", line 1, in <module>
File "/home/tom/pypy/site-packages/astropy/tests/runner.py", line 266, in test
return runner.run_tests(**kwargs)
File "/home/tom/pypy/site-packages/astropy/tests/runner.py", line 611, in run_tests
return super().run_tests(**kwargs)
File "/home/tom/pypy/site-packages/astropy/tests/runner.py", line 248, in run_tests
return pytest.main(args=args, plugins=plugins)
File "/home/tom/pypy/site-packages/_pytest/config/__init__.py", line 92, in main
config=config
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/main.py", line 239, in pytest_cmdline_main
return wrap_session(config, _main)
File "/home/tom/pypy/site-packages/_pytest/main.py", line 196, in wrap_session
session.exitstatus = doit(config, session) or 0
File "/home/tom/pypy/site-packages/_pytest/main.py", line 246, in _main
config.hook.pytest_runtestloop(session=session)
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/main.py", line 270, in pytest_runtestloop
item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 81, in pytest_runtest_protocol
runtestprotocol(item, nextitem=nextitem)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 96, in runtestprotocol
reports.append(call_and_report(item, "call", log))
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 182, in call_and_report
call = call_runtest_hook(item, when, **kwds)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 207, in call_runtest_hook
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 234, in from_call
result = func()
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 207, in <lambda>
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/runner.py", line 131, in pytest_runtest_call
item.runtest()
File "/home/tom/pypy/site-packages/_pytest/python.py", line 1435, in runtest
self.ihook.pytest_pyfunc_call(pyfuncitem=self)
File "/home/tom/pypy/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/tom/pypy/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/home/tom/pypy/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/tom/pypy/site-packages/_pytest/python.py", line 166, in pytest_pyfunc_call
result = testfunction(**testargs)
File "/home/tom/pypy/site-packages/astropy/io/fits/tests/test_fitscheck.py", line 23, in test_valid_file
assert fitscheck.main([testfile]) == 0
File "/home/tom/pypy/site-packages/astropy/io/fits/scripts/fitscheck.py", line 215, in main
log.warning(f'{errors} errors')
Message: '1 errors'
Arguments: ()
1 errors
------------------------------ Captured log call -------------------------------
ERROR fitscheck:fitscheck.py:199 EXCEPTION '/home/tom/pypy/site-packages/astropy/io/fits/tests/data/checksum.fits' .. module 'sys' has no attribute 'getrefcount'
WARNING fitscheck:fitscheck.py:215 1 errors
_____________________ TestFitscheck.test_overwrite_invalid _____________________
self = <astropy.io.fits.tests.test_fitscheck.TestFitscheck object at 0x000000000b8fd750>
capsys = <_pytest.capture.CaptureFixture object at 0x000000000b8fc138>
def test_overwrite_invalid(self, capsys):
"""
Tests that invalid checksum or datasum are overwriten when the file is
saved.
"""
reffile = self.temp('ref.fits')
with fits.open(self.data('tb.fits')) as hdul:
> hdul.writeto(reffile, checksum=True)
pypy/site-packages/astropy/io/fits/tests/test_fitscheck.py:56:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________ TestFITSDiff_script.test_nodiff ________________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x000000000ade9520>
def test_nodiff(self):
a = np.arange(100).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main([tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________ TestFITSDiff_script.test_onediff _______________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000012a7d8d8>
def test_onediff(self):
a = np.arange(100).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
b[1, 0] = 12
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main([tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:53:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestFITSDiff_script.test_manydiff _______________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000018975fa0>
capsys = <_pytest.capture.CaptureFixture object at 0x0000000018974e90>
def test_manydiff(self, capsys):
a = np.arange(100).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a + 1
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main([tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:66:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestFITSDiff_script.test_outputfile ______________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000013975168>
def test_outputfile(self):
a = np.arange(100).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
b[1, 0] = 12
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main(['-o', self.temp('diff.txt'), tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:95:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestFITSDiff_script.test_atol _________________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x000000001ab0d600>
def test_atol(self):
a = np.arange(100, dtype=float).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
b[1, 0] = 11
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main(["-a", "1", tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestFITSDiff_script.test_rtol _________________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x00000000170d8c28>
def test_rtol(self):
a = np.arange(100, dtype=float).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
b[1, 0] = 11
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main(["-r", "1e-1", tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:132:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestFITSDiff_script.test_rtol_diff ______________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000014c75ef8>
capsys = <_pytest.capture.CaptureFixture object at 0x0000000014c75b08>
def test_rtol_diff(self, capsys):
a = np.arange(100, dtype=float).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
b[1, 0] = 11
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main(["-r", "1e-2", tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:145:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestFITSDiff_script.test_not_quiet ______________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000015219248>
capsys = <_pytest.capture.CaptureFixture object at 0x00000000152186e8>
def test_not_quiet(self, capsys):
a = np.arange(100).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main([tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:179:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestFITSDiff_script.test_quiet ________________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000010eb0f00>
capsys = <_pytest.capture.CaptureFixture object at 0x0000000010eb0ad8>
def test_quiet(self, capsys):
a = np.arange(100).reshape(10, 10)
hdu_a = PrimaryHDU(data=a)
b = a.copy()
hdu_b = PrimaryHDU(data=b)
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdu_a.writeto(tmp_a)
hdu_b.writeto(tmp_b)
> numdiff = fitsdiff.main(["-q", tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestFITSDiff_script.test_path _________________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000013430090>
capsys = <_pytest.capture.CaptureFixture object at 0x00000000134935c8>
def test_path(self, capsys):
os.mkdir(self.temp('sub/'))
tmp_b = self.temp('sub/ascii.fits')
tmp_g = self.temp('sub/group.fits')
tmp_h = self.data('group.fits')
with hdulist.fitsopen(tmp_h) as hdu_b:
> hdu_b.writeto(tmp_g)
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:214:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestFITSDiff_script.test_ignore_hdus _____________________
self = <astropy.io.fits.tests.test_fitsdiff.TestFITSDiff_script object at 0x0000000011ae0c60>
def test_ignore_hdus(self):
a = np.arange(100).reshape(10, 10)
b = a.copy() + 1
ha = Header([('A', 1), ('B', 2), ('C', 3)])
phdu_a = PrimaryHDU(header=ha)
phdu_b = PrimaryHDU(header=ha)
ihdu_a = ImageHDU(data=a, name='SCI')
ihdu_b = ImageHDU(data=b, name='SCI')
hdulist_a = HDUList([phdu_a, ihdu_a])
hdulist_b = HDUList([phdu_b, ihdu_b])
tmp_a = self.temp('testa.fits')
tmp_b = self.temp('testb.fits')
hdulist_a.writeto(tmp_a)
hdulist_b.writeto(tmp_b)
> numdiff = fitsdiff.main([tmp_a, tmp_b])
pypy/site-packages/astropy/io/fits/tests/test_fitsdiff.py:263:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/scripts/fitsdiff.py:322: in main
ignore_blank_cards=opts.ignore_blank_cards)
pypy/site-packages/astropy/io/fits/diff.py:318: in __init__
a.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestGroupsFunctions.test_open _________________________
self = <astropy.io.fits.tests.test_groups.TestGroupsFunctions object at 0x000000000d699ad0>
def test_open(self):
with fits.open(self.data('random_groups.fits')) as hdul:
assert isinstance(hdul[0], fits.GroupsHDU)
naxes = (3, 1, 128, 1, 1)
parameters = ['UU', 'VV', 'WW', 'BASELINE', 'DATE']
info = [(0, 'PRIMARY', 1, 'GroupsHDU', 147, naxes, 'float32',
'3 Groups 5 Parameters')]
assert hdul.info(output=False) == info
ghdu = hdul[0]
assert ghdu.parnames == parameters
assert list(ghdu.data.dtype.names) == parameters + ['DATA']
assert isinstance(ghdu.data, fits.GroupData)
# The data should be equal to the number of groups
assert ghdu.header['GCOUNT'] == len(ghdu.data)
assert ghdu.data.data.shape == (len(ghdu.data),) + naxes[::-1]
assert ghdu.data.parnames == parameters
assert isinstance(ghdu.data[0], fits.Group)
assert len(ghdu.data[0]) == len(parameters) + 1
assert ghdu.data[0].data.shape == naxes[::-1]
> assert ghdu.data[0].parnames == parameters
pypy/site-packages/astropy/io/fits/tests/test_groups.py:37:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestGroupsFunctions.test_random_groups_data_update ______________
self = <astropy.io.fits.tests.test_groups.TestGroupsFunctions object at 0x000000000b0bf638>
def test_random_groups_data_update(self):
"""
Regression test for https://github.com/astropy/astropy/issues/3730 and
for https://github.com/spacetelescope/PyFITS/issues/102
"""
self.copy_file('random_groups.fits')
with fits.open(self.temp('random_groups.fits'), mode='update') as h:
> h[0].data['UU'] = 0.42
pypy/site-packages/astropy/io/fits/tests/test_groups.py:70:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestGroupsFunctions.test_parnames_round_trip _________________
self = <astropy.io.fits.tests.test_groups.TestGroupsFunctions object at 0x00007f587b845088>
def test_parnames_round_trip(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/130
Ensures that opening a random groups file in update mode or writing it
to a new file does not cause any change to the parameter names.
"""
# Because this test tries to update the random_groups.fits file, let's
# make a copy of it first (so that the file doesn't actually get
# modified in the off chance that the test fails
self.copy_file('random_groups.fits')
parameters = ['UU', 'VV', 'WW', 'BASELINE', 'DATE']
with fits.open(self.temp('random_groups.fits'), mode='update') as h:
assert h[0].parnames == parameters
h.flush()
# Open again just in read-only mode to ensure the parnames didn't
# change
with fits.open(self.temp('random_groups.fits')) as h:
assert h[0].parnames == parameters
> h.writeto(self.temp('test.fits'))
pypy/site-packages/astropy/io/fits/tests/test_groups.py:96:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestGroupsFunctions.test_groupdata_slice ___________________
self = <astropy.io.fits.tests.test_groups.TestGroupsFunctions object at 0x000000000b6a1050>
def test_groupdata_slice(self):
"""
A simple test to ensure that slicing GroupData returns a new, smaller
GroupData object, as is the case with a normal FITS_rec. This is a
regression test for an as-of-yet unreported issue where slicing
GroupData returned a single Group record.
"""
with fits.open(self.data('random_groups.fits')) as hdul:
s = hdul[0].data[1:]
assert isinstance(s, fits.GroupData)
assert len(s) == 2
> assert hdul[0].data.parnames == s.parnames
pypy/site-packages/astropy/io/fits/tests/test_groups.py:113:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestGroupsFunctions.test_group_slice _____________________
self = <astropy.io.fits.tests.test_groups.TestGroupsFunctions object at 0x000000000d3c7210>
def test_group_slice(self):
"""
Tests basic slicing a single group record.
"""
# A very basic slice test
with fits.open(self.data('random_groups.fits')) as hdul:
g = hdul[0].data[0]
s = g[2:4]
assert len(s) == 2
assert s[0] == g[2]
assert s[-1] == g[-3]
s = g[::-1]
assert len(s) == 6
assert (s[0] == g[-1]).all()
assert s[-1] == g[0]
s = g[::2]
assert len(s) == 3
assert s[0] == g[0]
assert s[1] == g[2]
> assert s[2] == g[4]
pypy/site-packages/astropy/io/fits/tests/test_groups.py:135:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestGroupsFunctions.test_create_groupdata ___________________
self = <astropy.io.fits.tests.test_groups.TestGroupsFunctions object at 0x000000000c2417c0>
def test_create_groupdata(self):
"""
Basic test for creating GroupData from scratch.
"""
imdata = np.arange(100.0)
imdata.shape = (10, 1, 1, 2, 5)
pdata1 = np.arange(10, dtype=np.float32) + 0.1
pdata2 = 42.0
x = fits.hdu.groups.GroupData(imdata, parnames=['abc', 'xyz'],
pardata=[pdata1, pdata2], bitpix=-32)
assert x.parnames == ['abc', 'xyz']
assert (x.par('abc') == pdata1).all()
assert (x.par('xyz') == ([pdata2] * len(x))).all()
assert (x.data == imdata).all()
# Test putting the data into a GroupsHDU and round-tripping it
ghdu = fits.GroupsHDU(data=x)
assert ghdu.parnames == ['abc', 'xyz']
assert ghdu.header['GCOUNT'] == 10
ghdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as h:
hdr = h[0].header
assert hdr['GCOUNT'] == 10
assert hdr['PCOUNT'] == 2
assert hdr['NAXIS'] == 5
assert hdr['NAXIS1'] == 0
assert hdr['NAXIS2'] == 5
assert hdr['NAXIS3'] == 2
assert hdr['NAXIS4'] == 1
assert hdr['NAXIS5'] == 1
assert h[0].data.parnames == ['abc', 'xyz']
> assert comparerecords(h[0].data, x)
pypy/site-packages/astropy/io/fits/tests/test_groups.py:171:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestHDUListFunctions.test_hdu_file_bytes ___________________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000001ec3c950>
def test_hdu_file_bytes(self):
with fits.open(self.data('checksum.fits')) as hdul:
res = hdul[0].filebytes()
assert res == 11520
res = hdul[1].filebytes()
> assert res == 8640
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:33:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestHDUListFunctions.test_hdulist_file_info __________________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x0000000016b0ea30>
def test_hdulist_file_info(self):
def test_fileinfo(**kwargs):
assert res['datSpan'] == kwargs.get('datSpan', 2880)
assert res['resized'] == kwargs.get('resized', False)
assert res['filename'] == self.data('checksum.fits')
assert res['datLoc'] == kwargs.get('datLoc', 8640)
assert res['hdrLoc'] == kwargs.get('hdrLoc', 0)
assert res['filemode'] == 'readonly'
with fits.open(self.data('checksum.fits')) as hdul:
res = hdul.fileinfo(0)
res = hdul.fileinfo(1)
test_fileinfo(datLoc=17280, hdrLoc=11520)
hdu = fits.ImageHDU(data=hdul[0].data)
hdul.insert(1, hdu)
res = hdul.fileinfo(0)
test_fileinfo(resized=True)
res = hdul.fileinfo(1)
test_fileinfo(datSpan=None, resized=True, datLoc=None, hdrLoc=None)
res = hdul.fileinfo(2)
> test_fileinfo(resized=1, datLoc=17280, hdrLoc=11520)
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:60:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________ TestHDUListFunctions.test_append_table_extension_to_empty_list ________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000001090f8d8>
def test_append_table_extension_to_empty_list(self):
"""Tests appending a Simple Table ExtensionHDU to a empty HDUList."""
hdul = fits.HDUList()
with fits.open(self.data('tb.fits')) as hdul1:
hdul.append(hdul1[1])
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 4, (), '', ''),
(1, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-append.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:110:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestHDUListFunctions.test_append_primary_to_non_empty_list __________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000160b4bb8>
def test_append_primary_to_non_empty_list(self):
"""Tests appending a Simple PrimaryHDU to a non-empty HDUList."""
with fits.open(self.data('arange.fits')) as hdul:
hdu = fits.PrimaryHDU(np.arange(100, dtype=np.int32))
hdul.append(hdu)
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 7, (11, 10, 7), 'int32', ''),
(1, '', 1, 'ImageHDU', 6, (100,), 'int32', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-append.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:142:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestHDUListFunctions.test_append_extension_to_non_empty_list _________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x0000000017076678>
def test_append_extension_to_non_empty_list(self):
"""Tests appending a Simple ExtensionHDU to a non-empty HDUList."""
with fits.open(self.data('tb.fits')) as hdul:
hdul.append(hdul[1])
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 11, (), '', ''),
(1, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', ''),
(2, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-append.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:158:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________ TestHDUListFunctions.test_insert_table_extension_to_empty_list ________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000163ff8d8>
def test_insert_table_extension_to_empty_list(self):
"""Tests inserting a Simple Table ExtensionHDU to a empty HDUList."""
hdul = fits.HDUList()
with fits.open(self.data('tb.fits')) as hdul1:
hdul.insert(0, hdul1[1])
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 4, (), '', ''),
(1, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-insert.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestHDUListFunctions.test_insert_primary_to_non_empty_list __________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000168cfec0>
def test_insert_primary_to_non_empty_list(self):
"""Tests inserting a Simple PrimaryHDU to a non-empty HDUList."""
with fits.open(self.data('arange.fits')) as hdul:
hdu = fits.PrimaryHDU(np.arange(100, dtype=np.int32))
hdul.insert(1, hdu)
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 7, (11, 10, 7), 'int32', ''),
(1, '', 1, 'ImageHDU', 6, (100,), 'int32', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-insert.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:245:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestHDUListFunctions.test_insert_extension_to_non_empty_list _________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000000c9ec640>
def test_insert_extension_to_non_empty_list(self):
"""Tests inserting a Simple ExtensionHDU to a non-empty HDUList."""
with fits.open(self.data('tb.fits')) as hdul:
hdul.insert(1, hdul[1])
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 11, (), '', ''),
(1, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', ''),
(2, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-insert.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:261:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___ TestHDUListFunctions.test_insert_extension_to_primary_in_non_empty_list ____
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000124a2410>
def test_insert_extension_to_primary_in_non_empty_list(self):
# Tests inserting a Simple ExtensionHDU to a non-empty HDUList.
with fits.open(self.data('tb.fits')) as hdul:
hdul.insert(0, hdul[1])
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 4, (), '', ''),
(1, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', ''),
(2, '', 1, 'ImageHDU', 12, (), '', ''),
(3, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-insert.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:312:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ TestHDUListFunctions.test_insert_image_extension_to_primary_in_non_empty_list _
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000161a60c8>
def test_insert_image_extension_to_primary_in_non_empty_list(self):
"""
Tests inserting a Simple Image ExtensionHDU to a non-empty HDUList
as the primary HDU.
"""
with fits.open(self.data('tb.fits')) as hdul:
hdu = fits.ImageHDU(np.arange(100, dtype=np.int32))
hdul.insert(0, hdu)
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 5, (100,), 'int32', ''),
(1, '', 1, 'ImageHDU', 12, (), '', ''),
(2, '', 1, 'BinTableHDU', 24, '2R x 4C', '[1J, 3A, 1E, 1L]', '')]
assert hdul.info(output=False) == info
> hdul.writeto(self.temp('test-insert.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:332:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestHDUListFunctions.test_update_filelike ___________________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x0000000022d771d8>
def test_update_filelike(self):
"""Test opening a file-like object in update mode and resizing the
HDU.
"""
sf = io.BytesIO()
arr = np.zeros((100, 100))
hdu = fits.PrimaryHDU(data=arr)
hdu.writeto(sf)
sf.seek(0)
arr = np.zeros((200, 200))
hdul = fits.open(sf, mode='update')
hdul[0].data = arr
> hdul.flush()
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:448:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/util.py:241: in wrapped
func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842: in flush
self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258: in _flush_update
self._flush_resize()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1372: in _flush_resize
hdulist.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestHDUListFunctions.test_replace_memmaped_array _______________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x0000000022199980>
def test_replace_memmaped_array(self):
# Copy the original before we modify it
with fits.open(self.data('test0.fits')) as hdul:
> hdul.writeto(self.temp('temp.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:543:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestHDUListFunctions.test_open_file_with_end_padding _____________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x0000000011bc8758>
def test_open_file_with_end_padding(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/106
Open files with end padding bytes.
"""
with fits.open(self.data('test0.fits'),
do_not_scale_image_data=True) as hdul:
info = hdul.info(output=False)
> hdul.writeto(self.temp('temp.fits'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:562:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestHDUListFunctions.test_open_file_with_bad_header_padding __________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000001f19cde8>
def test_open_file_with_bad_header_padding(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/136
Open files with nulls for header block padding instead of spaces.
"""
a = np.arange(100).reshape(10, 10)
hdu = fits.PrimaryHDU(data=a)
hdu.writeto(self.temp('temp.fits'))
# Figure out where the header padding begins and fill it with nulls
end_card_pos = str(hdu.header).index('END' + ' ' * 77)
padding_start = end_card_pos + 80
padding_len = 2880 - padding_start
with open(self.temp('temp.fits'), 'r+b') as f:
f.seek(padding_start)
f.write('\0'.encode('ascii') * padding_len)
with catch_warnings(AstropyUserWarning) as w:
with fits.open(self.temp('temp.fits')) as hdul:
> assert (hdul[0].data == a).all()
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:592:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestHDUListFunctions.test_update_with_truncated_header ____________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000000b0bf8d8>
def test_update_with_truncated_header(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/148
Test that saving an update where the header is shorter than the
original header doesn't leave a stump from the old header in the file.
"""
data = np.arange(100)
hdu = fits.PrimaryHDU(data=data)
idx = 1
while len(hdu.header) < 34:
hdu.header[f'TEST{idx}'] = idx
idx += 1
hdu.writeto(self.temp('temp.fits'), checksum=True)
with fits.open(self.temp('temp.fits'), mode='update') as hdul:
# Modify the header, forcing it to be rewritten
> hdul[0].header['TEST1'] = 2
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:617:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestHDUListFunctions.test_update_resized_header ________________
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000c374678>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
> self.flush(output_verify=output_verify, verbose=verbose)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:963:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = ([<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000c374678>],)
kwargs = {'output_verify': 'exception', 'verbose': False}
curr_thread = <_MainThread(MainThread, started 140018066300352)>
single_thread = True
SigintHandler = <class 'astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler'>
sigint_handler = <astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler object at 0x000000000c375088>
old_handler = <built-in function default_int_handler>
@wraps(func)
def wrapped(*args, **kwargs):
# Get the name of the current thread and determine if this is a single
# threaded application
curr_thread = threading.currentThread()
single_thread = (threading.activeCount() == 1 and
curr_thread.getName() == 'MainThread')
class SigintHandler:
def __init__(self):
self.sigint_received = False
def __call__(self, signum, frame):
warnings.warn('KeyboardInterrupt ignored until {} is '
'complete!'.format(func.__name__),
AstropyUserWarning)
self.sigint_received = True
sigint_handler = SigintHandler()
# Define new signal interput handler
if single_thread:
# Install new handler
old_handler = signal.signal(signal.SIGINT, sigint_handler)
try:
> func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/util.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000c374678>]
output_verify = 'exception', verbose = False
@ignore_sigint
def flush(self, output_verify='fix', verbose=False):
"""
Force a write of the `HDUList` back to the file (for append and
update modes only).
Parameters
----------
output_verify : str
Output verification option. Must be one of ``"fix"``,
``"silentfix"``, ``"ignore"``, ``"warn"``, or
``"exception"``. May also be any combination of ``"fix"`` or
``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception"
(e.g. ``"fix+warn"``). See :ref:`verify` for more info.
verbose : bool
When `True`, print verbose messages
"""
if self._file.mode not in ('append', 'update', 'ostream'):
warnings.warn("Flush for '{}' mode is not supported."
.format(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 {} to {}.'.format(
filename, backup), AstropyUserWarning)
try:
shutil.copy(filename, backup)
except OSError as exc:
raise OSError('Failed to save backup to destination {}: '
'{}'.format(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)
with _free_space_check(self):
hdu._writeto(self._file)
if verbose:
print('append HDU', hdu.name, extver)
hdu._new = False
hdu._postwriteto()
elif self._file.mode == 'update':
> self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000c374678>]
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000c374678>]
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+')
elif self._file.compression == 'bzip2':
if not HAS_BZ2:
raise ModuleNotFoundError(
"This Python installation does not provide the bz2 module.")
new_file = bz2.BZ2File(name, mode='w')
else:
new_file = name
with self.fromfile(new_file, mode='append') as hdulist:
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1307:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000000c2ad440>
@pytest.mark.filterwarnings("ignore:Assigning the 'data' attribute is an "
"inherently unsafe operation")
def test_update_resized_header(self):
"""
Test saving updates to a file where the header is one block smaller
than before, and in the case where the heade ris one block larger than
before.
"""
data = np.arange(100)
hdu = fits.PrimaryHDU(data=data)
idx = 1
while len(str(hdu.header)) <= 2880:
hdu.header[f'TEST{idx}'] = idx
idx += 1
orig_header = hdu.header.copy()
hdu.writeto(self.temp('temp.fits'))
with fits.open(self.temp('temp.fits'), mode='update') as hdul:
while len(str(hdul[0].header)) > 2880:
> del hdul[0].header[-1]
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:645:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestHDUListFunctions.test_update_resized_header2 _______________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000203cf8a0>
def test_update_resized_header2(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/150
This is similar to test_update_resized_header, but specifically tests a
case of multiple consecutive flush() calls on the same HDUList object,
where each flush() requires a resize.
"""
data1 = np.arange(100)
data2 = np.arange(100) + 100
phdu = fits.PrimaryHDU(data=data1)
hdu = fits.ImageHDU(data=data2)
phdu.writeto(self.temp('temp.fits'))
with fits.open(self.temp('temp.fits'), mode='append') as hdul:
hdul.append(hdu)
with fits.open(self.temp('temp.fits'), mode='update') as hdul:
idx = 1
while len(str(hdul[0].header)) <= 2880 * 2:
hdul[0].header[f'TEST{idx}'] = idx
idx += 1
> hdul.flush()
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:688:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = ([<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>],)
kwargs = {}, curr_thread = <_MainThread(MainThread, started 140018066300352)>
single_thread = True
SigintHandler = <class 'astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler'>
sigint_handler = <astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler object at 0x0000000020529e50>
old_handler = <built-in function default_int_handler>
@wraps(func)
def wrapped(*args, **kwargs):
# Get the name of the current thread and determine if this is a single
# threaded application
curr_thread = threading.currentThread()
single_thread = (threading.activeCount() == 1 and
curr_thread.getName() == 'MainThread')
class SigintHandler:
def __init__(self):
self.sigint_received = False
def __call__(self, signum, frame):
warnings.warn('KeyboardInterrupt ignored until {} is '
'complete!'.format(func.__name__),
AstropyUserWarning)
self.sigint_received = True
sigint_handler = SigintHandler()
# Define new signal interput handler
if single_thread:
# Install new handler
old_handler = signal.signal(signal.SIGINT, sigint_handler)
try:
> func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/util.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
output_verify = 'fix', verbose = False
@ignore_sigint
def flush(self, output_verify='fix', verbose=False):
"""
Force a write of the `HDUList` back to the file (for append and
update modes only).
Parameters
----------
output_verify : str
Output verification option. Must be one of ``"fix"``,
``"silentfix"``, ``"ignore"``, ``"warn"``, or
``"exception"``. May also be any combination of ``"fix"`` or
``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception"
(e.g. ``"fix+warn"``). See :ref:`verify` for more info.
verbose : bool
When `True`, print verbose messages
"""
if self._file.mode not in ('append', 'update', 'ostream'):
warnings.warn("Flush for '{}' mode is not supported."
.format(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 {} to {}.'.format(
filename, backup), AstropyUserWarning)
try:
shutil.copy(filename, backup)
except OSError as exc:
raise OSError('Failed to save backup to destination {}: '
'{}'.format(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)
with _free_space_check(self):
hdu._writeto(self._file)
if verbose:
print('append HDU', hdu.name, extver)
hdu._new = False
hdu._postwriteto()
elif self._file.mode == 'update':
> self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
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+')
elif self._file.compression == 'bzip2':
if not HAS_BZ2:
raise ModuleNotFoundError(
"This Python installation does not provide the bz2 module.")
new_file = bz2.BZ2File(name, mode='w')
else:
new_file = name
with self.fromfile(new_file, mode='append') as hdulist:
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1307:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
> self.flush(output_verify=output_verify, verbose=verbose)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:963:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = ([<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>],)
kwargs = {'output_verify': 'exception', 'verbose': False}
curr_thread = <_MainThread(MainThread, started 140018066300352)>
single_thread = True
SigintHandler = <class 'astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler'>
sigint_handler = <astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler object at 0x00000000205eaaa0>
old_handler = <built-in function default_int_handler>
@wraps(func)
def wrapped(*args, **kwargs):
# Get the name of the current thread and determine if this is a single
# threaded application
curr_thread = threading.currentThread()
single_thread = (threading.activeCount() == 1 and
curr_thread.getName() == 'MainThread')
class SigintHandler:
def __init__(self):
self.sigint_received = False
def __call__(self, signum, frame):
warnings.warn('KeyboardInterrupt ignored until {} is '
'complete!'.format(func.__name__),
AstropyUserWarning)
self.sigint_received = True
sigint_handler = SigintHandler()
# Define new signal interput handler
if single_thread:
# Install new handler
old_handler = signal.signal(signal.SIGINT, sigint_handler)
try:
> func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/util.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
output_verify = 'exception', verbose = False
@ignore_sigint
def flush(self, output_verify='fix', verbose=False):
"""
Force a write of the `HDUList` back to the file (for append and
update modes only).
Parameters
----------
output_verify : str
Output verification option. Must be one of ``"fix"``,
``"silentfix"``, ``"ignore"``, ``"warn"``, or
``"exception"``. May also be any combination of ``"fix"`` or
``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception"
(e.g. ``"fix+warn"``). See :ref:`verify` for more info.
verbose : bool
When `True`, print verbose messages
"""
if self._file.mode not in ('append', 'update', 'ostream'):
warnings.warn("Flush for '{}' mode is not supported."
.format(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 {} to {}.'.format(
filename, backup), AstropyUserWarning)
try:
shutil.copy(filename, backup)
except OSError as exc:
raise OSError('Failed to save backup to destination {}: '
'{}'.format(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)
with _free_space_check(self):
hdu._writeto(self._file)
if verbose:
print('append HDU', hdu.name, extver)
hdu._new = False
hdu._postwriteto()
elif self._file.mode == 'update':
> self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>, <astropy.io.fits.hdu.image.ImageHDU object at 0x0000000020529f68>]
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+')
elif self._file.compression == 'bzip2':
if not HAS_BZ2:
raise ModuleNotFoundError(
"This Python installation does not provide the bz2 module.")
new_file = bz2.BZ2File(name, mode='w')
else:
new_file = name
with self.fromfile(new_file, mode='append') as hdulist:
for hdu in self:
> hdu._writeto(hdulist._file, inplace=True, copy=True)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1299:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>
fileobj = <astropy.io.fits.file._File <_io.FileIO [closed]>>, inplace = True
copy = True
def _writeto(self, fileobj, inplace=False, copy=False):
try:
dirname = os.path.dirname(fileobj._file.name)
except (AttributeError, TypeError):
dirname = None
with _free_space_check(self, dirname):
> self._writeto_internal(fileobj, inplace, copy)
pypy/site-packages/astropy/io/fits/hdu/base.py:674:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000020529168>
fileobj = <astropy.io.fits.file._File <_io.FileIO [closed]>>, inplace = True
copy = True
def _writeto_internal(self, fileobj, inplace, copy):
# For now fileobj is assumed to be a _File object
if not inplace or self._new:
header_offset, _ = self._writeheader(fileobj)
data_offset, data_size = self._writedata(fileobj)
# Set the various data location attributes on newly-written HDUs
if self._new:
self._header_offset = header_offset
self._data_offset = data_offset
self._data_size = data_size
return
hdrloc = self._header_offset
hdrsize = self._data_offset - self._header_offset
datloc = self._data_offset
datsize = self._data_size
if self._header._modified:
# Seek to the original header location in the file
> self._file.seek(hdrloc)
pypy/site-packages/astropy/io/fits/hdu/base.py:696:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, offset = 0
whence = 0
def seek(self, offset, whence=0):
if not hasattr(self._file, 'seek'):
return
> self._file.seek(offset, whence)
E ValueError: I/O operation on closed file
pypy/site-packages/astropy/io/fits/file.py:389: ValueError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000203cf8a0>
def test_update_resized_header2(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/150
This is similar to test_update_resized_header, but specifically tests a
case of multiple consecutive flush() calls on the same HDUList object,
where each flush() requires a resize.
"""
data1 = np.arange(100)
data2 = np.arange(100) + 100
phdu = fits.PrimaryHDU(data=data1)
hdu = fits.ImageHDU(data=data2)
phdu.writeto(self.temp('temp.fits'))
with fits.open(self.temp('temp.fits'), mode='append') as hdul:
hdul.append(hdu)
with fits.open(self.temp('temp.fits'), mode='update') as hdul:
idx = 1
while len(str(hdul[0].header)) <= 2880 * 2:
hdul[0].header[f'TEST{idx}'] = idx
idx += 1
hdul.flush()
> hdul.append(hdu)
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:689:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestHDUListFunctions.test_hdul_fromstring ___________________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000000d566fa8>
@ignore_warnings()
def test_hdul_fromstring(self):
"""
Test creating the HDUList structure in memory from a string containing
an entire FITS file. This is similar to test_hdu_fromstring but for an
entire multi-extension FITS file at once.
"""
# Tests HDUList.fromstring for all of Astropy's built in test files
def test_fromstring(filename):
with fits.open(filename) as hdul:
orig_info = hdul.info(output=False)
with open(filename, 'rb') as f:
dat = f.read()
hdul2 = fits.HDUList.fromstring(dat)
assert orig_info == hdul2.info(output=False)
for idx in range(len(hdul)):
assert hdul[idx].header == hdul2[idx].header
if hdul[idx].data is None or hdul2[idx].data is None:
assert hdul[idx].data == hdul2[idx].data
elif (hdul[idx].data.dtype.fields and
hdul2[idx].data.dtype.fields):
# Compare tables
for n in hdul[idx].data.names:
c1 = hdul[idx].data[n]
c2 = hdul2[idx].data[n]
assert (c1 == c2).all()
elif (any(dim == 0 for dim in hdul[idx].data.shape) or
any(dim == 0 for dim in hdul2[idx].data.shape)):
# For some reason some combinations of Python and Numpy
# on Windows result in MemoryErrors when trying to work
# on memmap arrays with more than one dimension but
# some dimensions of size zero, so include a special
# case for that
return hdul[idx].data.shape == hdul2[idx].data.shape
else:
np.testing.assert_array_equal(hdul[idx].data,
hdul2[idx].data)
for filename in glob.glob(os.path.join(self.data_dir, '*.fits')):
if sys.platform == 'win32' and filename == 'zerowidth.fits':
# Running this test on this file causes a crash in some
# versions of Numpy on Windows. See ticket:
# https://aeon.stsci.edu/ssb/trac/pyfits/ticket/174
continue
elif filename.endswith('variable_length_table.fits'):
# Comparing variable length arrays is non-trivial and thus
# skipped at this point.
# TODO: That's probably possible, so one could make it work.
continue
> test_fromstring(filename)
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:749:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:736: in test_fromstring
hdul2[idx].data)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestHDUListFunctions.test_save_backup _____________________
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x000000001451b050>
def test_save_backup(self):
"""Test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/121
Save backup of file before flushing changes.
"""
self.copy_file('scale.fits')
with ignore_warnings():
with fits.open(self.temp('scale.fits'), mode='update',
save_backup=True) as hdul:
# Make some changes to the original file to force its header
# and data to be rewritten
hdul[0].header['TEST'] = 'TEST'
> hdul[0].data[0] = 0
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:768:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestHDUListFunctions.test_replace_mmap_data __________________
mmap_a = True, mmap_b = True
def test(mmap_a, mmap_b):
hdu_a = fits.PrimaryHDU(data=arr_a)
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.PrimaryHDU(data=arr_b)
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'), mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
> hdul_a[0].data = hdul_b[0].data
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:809:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000013e3ec60>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000013e3ec60>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x0000000018c59948>
def test_replace_mmap_data(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/25
Replacing the mmap'd data of one file with mmap'd data from a
different file should work.
"""
arr_a = np.arange(10)
arr_b = arr_a * 2
def test(mmap_a, mmap_b):
hdu_a = fits.PrimaryHDU(data=arr_a)
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.PrimaryHDU(data=arr_b)
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'), mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
hdul_a[0].data = hdul_b[0].data
with fits.open(self.temp('test_a.fits')) as hdul_a:
assert np.all(hdul_a[0].data == arr_b)
with ignore_warnings():
> test(True, True)
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:815:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:809: in test
hdul_a[0].data = hdul_b[0].data
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:970: in close
hdu._close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/base.py:748: in _close
del self.data
pypy/site-packages/astropy/utils/decorators.py:765: in __delete__
self.fdel(obj)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000013e3e8e0>
def data(self):
# The deleter
if self._file is not None and self._data_loaded:
> data_refcount = sys.getrefcount(self.data)
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/hdu/base.py:117: AttributeError
________________ TestHDUListFunctions.test_replace_mmap_data_2 _________________
mmap_a = True, mmap_b = True
def test(mmap_a, mmap_b):
col_a = fits.Column(name='a', format='J', array=arr_a)
col_b = fits.Column(name='b', format='J', array=arr_b)
hdu_a = fits.BinTableHDU.from_columns([col_a])
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.BinTableHDU.from_columns([col_b])
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'), mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
> hdul_a[1].data = hdul_b[1].data
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:847:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x00000000220f78a0>, <astropy.io.fits.hdu.table.BinTableHDU object at 0x00000000220f6c60>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x00000000220f78a0>, <astropy.io.fits.hdu.table.BinTableHDU object at 0x00000000220f6c60>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_hdulist.TestHDUListFunctions object at 0x00000000134b6790>
def test_replace_mmap_data_2(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/25
Replacing the mmap'd data of one file with mmap'd data from a
different file should work. Like test_replace_mmap_data but with
table data instead of image data.
"""
arr_a = np.arange(10)
arr_b = arr_a * 2
def test(mmap_a, mmap_b):
col_a = fits.Column(name='a', format='J', array=arr_a)
col_b = fits.Column(name='b', format='J', array=arr_b)
hdu_a = fits.BinTableHDU.from_columns([col_a])
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.BinTableHDU.from_columns([col_b])
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'), mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
hdul_a[1].data = hdul_b[1].data
with fits.open(self.temp('test_a.fits')) as hdul_a:
assert 'b' in hdul_a[1].columns.names
assert 'a' not in hdul_a[1].columns.names
assert np.all(hdul_a[1].data['b'] == arr_b)
with ignore_warnings():
> test(True, True)
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:855:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py:847: in test
hdul_a[1].data = hdul_b[1].data
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:970: in close
hdu._close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/base.py:748: in _close
del self.data
pypy/site-packages/astropy/utils/decorators.py:765: in __delete__
self.fdel(obj)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.table.BinTableHDU object at 0x00000000220f6de8>
def data(self):
# The deleter
if self._file is not None and self._data_loaded:
> data_refcount = sys.getrefcount(self.data)
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/hdu/base.py:117: AttributeError
___________________ TestHeaderFunctions.test_update_comment ____________________
self = <astropy.io.fits.tests.test_header.TestHeaderFunctions object at 0x0000000016179fa0>
def test_update_comment(self):
hdul = fits.open(self.data('arange.fits'))
hdul[0].header.update({'FOO': ('BAR', 'BAZ')})
assert hdul[0].header['FOO'] == 'BAR'
assert hdul[0].header.comments['FOO'] == 'BAZ'
with pytest.raises(ValueError):
hdul[0].header.update({'FOO2': ('BAR', 'BAZ', 'EXTRA')})
hdul.writeto(self.temp('test.fits'))
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_header.py:248:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestHeaderFunctions.test_end_in_comment ____________________
self = <astropy.io.fits.tests.test_header.TestHeaderFunctions object at 0x0000000011aea368>
def test_end_in_comment(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/142
Tests a case where the comment of a card ends with END, and is followed
by several blank cards.
"""
data = np.arange(100).reshape(10, 10)
hdu = fits.PrimaryHDU(data=data)
hdu.header['TESTKW'] = ('Test val', 'This is the END')
# Add a couple blanks after the END string
hdu.header.append()
hdu.header.append()
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits'), memmap=False) as hdul:
# memmap = False to avoid leaving open a mmap to the file when we
# access the data--this causes problems on Windows when we try to
# overwrite the file later
assert 'TESTKW' in hdul[0].header
assert hdul[0].header == hdu.header
assert (hdul[0].data == data).all()
# Add blanks until the header is extended to two block sizes
while len(hdu.header) < 36:
hdu.header.append()
with ignore_warnings():
hdu.writeto(self.temp('test.fits'), overwrite=True)
with fits.open(self.temp('test.fits')) as hdul:
assert 'TESTKW' in hdul[0].header
assert hdul[0].header == hdu.header
> assert (hdul[0].data == data).all()
pypy/site-packages/astropy/io/fits/tests/test_header.py:2023:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestImageFunctions.test_fortran_array _____________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000022716838>
def test_fortran_array(self):
# Test that files are being correctly written+read for "C" and "F" order arrays
a = np.arange(21).reshape(3,7)
b = np.asfortranarray(a)
afits = self.temp('a_str.fits')
bfits = self.temp('b_str.fits')
# writting to str specified files
fits.PrimaryHDU(data=a).writeto(afits)
fits.PrimaryHDU(data=b).writeto(bfits)
> np.testing.assert_array_equal(fits.getdata(afits), a)
pypy/site-packages/astropy/io/fits/tests/test_image.py:178:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestImageFunctions.test_fortran_array_non_contiguous _____________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000001aa90288>
def test_fortran_array_non_contiguous(self):
# Test that files are being correctly written+read for 'C' and 'F' order arrays
a = np.arange(105).reshape(3,5,7)
b = np.asfortranarray(a)
# writting to str specified files
afits = self.temp('a_str_slice.fits')
bfits = self.temp('b_str_slice.fits')
fits.PrimaryHDU(data=a[::2, ::2]).writeto(afits)
fits.PrimaryHDU(data=b[::2, ::2]).writeto(bfits)
> np.testing.assert_array_equal(fits.getdata(afits), a[::2, ::2])
pypy/site-packages/astropy/io/fits/tests/test_image.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestImageFunctions.test_io_manipulation ____________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000000dd141e0>
@pytest.mark.filterwarnings("ignore:Assigning the 'data' attribute is an "
"inherently unsafe operation")
def test_io_manipulation(self):
# Get a keyword value. An extension can be referred by name or by
# number. Both extension and keyword names are case insensitive.
with fits.open(self.data('test0.fits')) as r:
assert r['primary'].header['naxis'] == 0
assert r[0].header['naxis'] == 0
# If there are more than one extension with the same EXTNAME value,
# the EXTVER can be used (as the second argument) to distinguish
# the extension.
assert r['sci', 1].header['detector'] == 1
# append (using "update()") a new card
r[0].header['xxx'] = 1.234e56
assert ('\n'.join(str(x) for x in r[0].header.cards[-3:]) ==
"EXPFLAG = 'NORMAL ' / Exposure interruption indicator \n"
"FILENAME= 'vtest3.fits' / File name \n"
"XXX = 1.234E+56 ")
# rename a keyword
r[0].header.rename_keyword('filename', 'fname')
pytest.raises(ValueError, r[0].header.rename_keyword, 'fname',
'history')
pytest.raises(ValueError, r[0].header.rename_keyword, 'fname',
'simple')
r[0].header.rename_keyword('fname', 'filename')
# get a subsection of data
assert np.array_equal(r[2].data[:3, :3],
np.array([[349, 349, 348],
[349, 349, 347],
[347, 350, 349]], dtype=np.int16))
# We can create a new FITS file by opening a new file with "append"
# mode.
with fits.open(self.temp('test_new.fits'), mode='append') as n:
# Append the primary header and the 2nd extension to the new
# file.
n.append(r[0])
n.append(r[2])
# The flush method will write the current HDUList object back
# to the newly created file on disk. The HDUList is still open
# and can be further operated.
n.flush()
assert n[1].data[1, 1] == 349
# modify a data point
> n[1].data[1, 1] = 99
pypy/site-packages/astropy/io/fits/tests/test_image.py:297:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000dceb6a8>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000dd56ec8>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000dceb6a8>, <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000dd56ec8>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and 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)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:970:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000dd56ec8>
closed = True
def _close(self, closed=True):
# If the data was mmap'd, close the underlying mmap (this will
# prevent any future access to the .data attribute if there are
# not other references to it; if there are other references then
# it is up to the user to clean those up
if (closed and self._data_loaded and
_get_array_mmap(self.data) is not None):
> del self.data
pypy/site-packages/astropy/io/fits/hdu/base.py:748:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.utils.decorators.lazyproperty object at 0x00007f587adbe7a0>
obj = <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000dd56ec8>
def __delete__(self, obj):
if self.fdel:
> self.fdel(obj)
pypy/site-packages/astropy/utils/decorators.py:765:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.hdu.image.ImageHDU object at 0x000000000dd56ec8>
def data(self):
# The deleter
if self._file is not None and self._data_loaded:
> data_refcount = sys.getrefcount(self.data)
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/hdu/base.py:117: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000000dd141e0>
@pytest.mark.filterwarnings("ignore:Assigning the 'data' attribute is an "
"inherently unsafe operation")
def test_io_manipulation(self):
# Get a keyword value. An extension can be referred by name or by
# number. Both extension and keyword names are case insensitive.
with fits.open(self.data('test0.fits')) as r:
assert r['primary'].header['naxis'] == 0
assert r[0].header['naxis'] == 0
# If there are more than one extension with the same EXTNAME value,
# the EXTVER can be used (as the second argument) to distinguish
# the extension.
assert r['sci', 1].header['detector'] == 1
# append (using "update()") a new card
r[0].header['xxx'] = 1.234e56
assert ('\n'.join(str(x) for x in r[0].header.cards[-3:]) ==
"EXPFLAG = 'NORMAL ' / Exposure interruption indicator \n"
"FILENAME= 'vtest3.fits' / File name \n"
"XXX = 1.234E+56 ")
# rename a keyword
r[0].header.rename_keyword('filename', 'fname')
pytest.raises(ValueError, r[0].header.rename_keyword, 'fname',
'history')
pytest.raises(ValueError, r[0].header.rename_keyword, 'fname',
'simple')
r[0].header.rename_keyword('fname', 'filename')
# get a subsection of data
assert np.array_equal(r[2].data[:3, :3],
np.array([[349, 349, 348],
[349, 349, 347],
[347, 350, 349]], dtype=np.int16))
# We can create a new FITS file by opening a new file with "append"
# mode.
with fits.open(self.temp('test_new.fits'), mode='append') as n:
# Append the primary header and the 2nd extension to the new
# file.
n.append(r[0])
n.append(r[2])
# The flush method will write the current HDUList object back
# to the newly created file on disk. The HDUList is still open
# and can be further operated.
n.flush()
assert n[1].data[1, 1] == 349
# modify a data point
n[1].data[1, 1] = 99
# When the file is closed, the most recent additions of
# extension(s) since last flush() will be appended, but any HDU
# already existed at the last flush will not be modified
del n
# If an existing file is opened with "append" mode, like the
# readonly mode, the HDU's will be read into the HDUList which can
# be modified in memory but can not be written back to the original
# file. A file opened with append mode can only add new HDU's.
os.rename(self.temp('test_new.fits'),
self.temp('test_append.fits'))
with fits.open(self.temp('test_append.fits'), mode='append') as a:
# The above change did not take effect since this was made
# after the flush().
assert a[1].data[1, 1] == 349
a.append(r[1])
del a
# When changes are made to an HDUList which was opened with
# "update" mode, they will be written back to the original file
# when a flush/close is called.
os.rename(self.temp('test_append.fits'),
self.temp('test_update.fits'))
with fits.open(self.temp('test_update.fits'), mode='update') as u:
# When the changes do not alter the size structures of the
# original (or since last flush) HDUList, the changes are
# written back "in place".
assert u[0].header['rootname'] == 'U2EQ0201T'
u[0].header['rootname'] = 'abc'
assert u[1].data[1, 1] == 349
u[1].data[1, 1] = 99
u.flush()
# If the changes affect the size structure, e.g. adding or
# deleting HDU(s), header was expanded or reduced beyond
# existing number of blocks (2880 bytes in each block), or
# change the data size, the HDUList is written to a temporary
# file, the original file is deleted, and the temporary file is
# renamed to the original file name and reopened in the update
# mode. To a user, these two kinds of updating writeback seem
# to be the same, unless the optional argument in flush or
# close is set to 1.
del u[2]
u.flush()
# The write method in HDUList class writes the current HDUList,
# with all changes made up to now, to a new file. This method
# works the same disregard the mode the HDUList was opened
# with.
u.append(r[3])
u.writeto(self.temp('test_new.fits'))
> del u
pypy/site-packages/astropy/io/fits/tests/test_image.py:354:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________ TestImageFunctions.test_section ________________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000000cc66368>
def test_section(self):
# section testing
fs = fits.open(self.data('arange.fits'))
assert np.array_equal(fs[0].section[3, 2, 5], 357)
assert np.array_equal(
fs[0].section[3, 2, :],
np.array([352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362]))
assert np.array_equal(fs[0].section[3, 2, 4:],
np.array([356, 357, 358, 359, 360, 361, 362]))
assert np.array_equal(fs[0].section[3, 2, :8],
np.array([352, 353, 354, 355, 356, 357, 358, 359]))
assert np.array_equal(fs[0].section[3, 2, -8:8],
np.array([355, 356, 357, 358, 359]))
assert np.array_equal(
fs[0].section[3, 2:5, :],
np.array([[352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362],
[363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373],
[374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384]]))
assert np.array_equal(fs[0].section[3, :, :][:3, :3],
np.array([[330, 331, 332],
[341, 342, 343],
[352, 353, 354]]))
dat = fs[0].data
assert np.array_equal(fs[0].section[3, 2:5, :8], dat[3, 2:5, :8])
assert np.array_equal(fs[0].section[3, 2:5, 3], dat[3, 2:5, 3])
assert np.array_equal(fs[0].section[3:6, :, :][:3, :3, :3],
np.array([[[330, 331, 332],
[341, 342, 343],
[352, 353, 354]],
[[440, 441, 442],
[451, 452, 453],
[462, 463, 464]],
[[550, 551, 552],
[561, 562, 563],
[572, 573, 574]]]))
assert np.array_equal(fs[0].section[:, :, :][:3, :2, :2],
np.array([[[0, 1],
[11, 12]],
[[110, 111],
[121, 122]],
[[220, 221],
[231, 232]]]))
assert np.array_equal(fs[0].section[:, 2, :], dat[:, 2, :])
assert np.array_equal(fs[0].section[:, 2:5, :], dat[:, 2:5, :])
assert np.array_equal(fs[0].section[3:6, 3, :], dat[3:6, 3, :])
assert np.array_equal(fs[0].section[3:6, 3:7, :], dat[3:6, 3:7, :])
assert np.array_equal(fs[0].section[:, ::2], dat[:, ::2])
assert np.array_equal(fs[0].section[:, [1, 2, 4], 3],
dat[:, [1, 2, 4], 3])
bool_index = np.array([True, False, True, True, False,
False, True, True, False, True])
assert np.array_equal(fs[0].section[:, bool_index, :],
dat[:, bool_index, :])
assert np.array_equal(
fs[0].section[3:6, 3, :, ...], dat[3:6, 3, :, ...])
assert np.array_equal(fs[0].section[..., ::2], dat[..., ::2])
assert np.array_equal(fs[0].section[..., [1, 2, 4], 3],
dat[..., [1, 2, 4], 3])
> fs.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:472:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestImageFunctions.test_section_data_single __________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000001b013050>
def test_section_data_single(self):
a = np.array([1])
hdu = fits.PrimaryHDU(a)
hdu.writeto(self.temp('test_new.fits'))
hdul = fits.open(self.temp('test_new.fits'))
sec = hdul[0].section
dat = hdul[0].data
assert np.array_equal(sec[0], dat[0])
assert np.array_equal(sec[...], dat[...])
assert np.array_equal(sec[..., 0], dat[..., 0])
assert np.array_equal(sec[0, ...], dat[0, ...])
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestImageFunctions.test_section_data_square __________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000201f1788>
def test_section_data_square(self):
a = np.arange(4).reshape(2, 2)
hdu = fits.PrimaryHDU(a)
hdu.writeto(self.temp('test_new.fits'))
hdul = fits.open(self.temp('test_new.fits'))
d = hdul[0]
dat = hdul[0].data
assert (d.section[:, :] == dat[:, :]).all()
assert (d.section[0, :] == dat[0, :]).all()
assert (d.section[1, :] == dat[1, :]).all()
assert (d.section[:, 0] == dat[:, 0]).all()
assert (d.section[:, 1] == dat[:, 1]).all()
assert (d.section[0, 0] == dat[0, 0]).all()
assert (d.section[0, 1] == dat[0, 1]).all()
assert (d.section[1, 0] == dat[1, 0]).all()
assert (d.section[1, 1] == dat[1, 1]).all()
assert (d.section[0:1, 0:1] == dat[0:1, 0:1]).all()
assert (d.section[0:2, 0:1] == dat[0:2, 0:1]).all()
assert (d.section[0:1, 0:2] == dat[0:1, 0:2]).all()
assert (d.section[0:2, 0:2] == dat[0:2, 0:2]).all()
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:509:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestImageFunctions.test_section_data_cube ___________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000001ab0d6a8>
def test_section_data_cube(self):
a = np.arange(18).reshape(2, 3, 3)
hdu = fits.PrimaryHDU(a)
hdu.writeto(self.temp('test_new.fits'))
hdul = fits.open(self.temp('test_new.fits'))
d = hdul[0]
dat = hdul[0].data
assert (d.section[:] == dat[:]).all()
assert (d.section[:, :] == dat[:, :]).all()
# Test that various combinations of indexing on the section are equal to
# indexing the data.
# Testing all combinations of scalar-index and [:] for each dimension.
for idx1 in [slice(None), 0, 1]:
for idx2 in [slice(None), 0, 1, 2]:
for idx3 in [slice(None), 0, 1, 2]:
nd_idx = (idx1, idx2, idx3)
assert (d.section[nd_idx] == dat[nd_idx]).all()
# Test all ways to slice the last dimension but keeping the first two.
for idx3 in [slice(0, 1), slice(0, 2), slice(0, 3),
slice(1, 2), slice(1, 3), slice(2, 3)]:
nd_idx = (slice(None), slice(None), idx3)
assert (d.section[nd_idx] == dat[nd_idx]).all()
# Test various combinations (not exhaustive) to slice all dimensions.
for idx1 in [slice(0, 1), slice(1, 2)]:
for idx2 in [slice(0, 1), slice(0, 2), slice(0, 3),
slice(1, 2), slice(1, 3)]:
for idx3 in [slice(0, 1), slice(0, 2), slice(0, 3),
slice(1, 2), slice(1, 3), slice(2, 3)]:
nd_idx = (idx1, idx2, idx3)
assert (d.section[nd_idx] == dat[nd_idx]).all()
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:547:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestImageFunctions.test_section_data_four ___________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000117b5bb0>
def test_section_data_four(self):
a = np.arange(256).reshape(4, 4, 4, 4)
hdu = fits.PrimaryHDU(a)
hdu.writeto(self.temp('test_new.fits'))
hdul = fits.open(self.temp('test_new.fits'))
d = hdul[0]
dat = hdul[0].data
assert (d.section[:, :, :, :] == dat[:, :, :, :]).all()
assert (d.section[:, :, :] == dat[:, :, :]).all()
assert (d.section[:, :] == dat[:, :]).all()
assert (d.section[:] == dat[:]).all()
assert (d.section[0, :, :, :] == dat[0, :, :, :]).all()
assert (d.section[0, :, 0, :] == dat[0, :, 0, :]).all()
assert (d.section[:, :, 0, :] == dat[:, :, 0, :]).all()
assert (d.section[:, 1, 0, :] == dat[:, 1, 0, :]).all()
assert (d.section[:, :, :, 1] == dat[:, :, :, 1]).all()
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:566:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestImageFunctions.test_section_data_scaled __________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000141d8138>
def test_section_data_scaled(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/143
This is like test_section_data_square but uses a file containing scaled
image data, to test that sections can work correctly with scaled data.
"""
hdul = fits.open(self.data('scale.fits'))
d = hdul[0]
dat = hdul[0].data
assert (d.section[:, :] == dat[:, :]).all()
assert (d.section[0, :] == dat[0, :]).all()
assert (d.section[1, :] == dat[1, :]).all()
assert (d.section[:, 0] == dat[:, 0]).all()
assert (d.section[:, 1] == dat[:, 1]).all()
assert (d.section[0, 0] == dat[0, 0]).all()
assert (d.section[0, 1] == dat[0, 1]).all()
assert (d.section[1, 0] == dat[1, 0]).all()
assert (d.section[1, 1] == dat[1, 1]).all()
assert (d.section[0:1, 0:1] == dat[0:1, 0:1]).all()
assert (d.section[0:2, 0:1] == dat[0:2, 0:1]).all()
assert (d.section[0:1, 0:2] == dat[0:1, 0:2]).all()
assert (d.section[0:2, 0:2] == dat[0:2, 0:2]).all()
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:592:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestImageFunctions.test_do_not_scale_image_data ________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000018406870>
def test_do_not_scale_image_data(self):
with fits.open(self.data('scale.fits'), do_not_scale_image_data=True) as hdul:
> assert hdul[0].data.dtype == np.dtype('>i2')
pypy/site-packages/astropy/io/fits/tests/test_image.py:615:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestImageFunctions.test_append_uint_data ___________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000133ec838>
def test_append_uint_data(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/56
(BZERO and BSCALE added in the wrong location when appending scaled
data)
"""
fits.writeto(self.temp('test_new.fits'), data=np.array([],
dtype='uint8'))
d = np.zeros([100, 100]).astype('uint16')
fits.append(self.temp('test_new.fits'), data=d)
with fits.open(self.temp('test_new.fits'), uint=True) as f:
> assert f[1].data.dtype == 'uint16'
pypy/site-packages/astropy/io/fits/tests/test_image.py:632:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestImageFunctions.test_uint_header_consistency ________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000022856758>
def test_uint_header_consistency(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2305
This ensures that an HDU containing unsigned integer data always has
the apppriate BZERO value in its header.
"""
for int_size in (16, 32, 64):
# Just make an array of some unsigned ints that wouldn't fit in a
# signed int array of the same bit width
max_uint = (2 ** int_size) - 1
if int_size == 64:
max_uint = np.uint64(int_size)
dtype = f'uint{int_size}'
arr = np.empty(100, dtype=dtype)
arr.fill(max_uint)
arr -= np.arange(100, dtype=dtype)
uint_hdu = fits.PrimaryHDU(data=arr)
assert np.all(uint_hdu.data == arr)
assert uint_hdu.data.dtype.name == f'uint{int_size}'
assert 'BZERO' in uint_hdu.header
assert uint_hdu.header['BZERO'] == (2 ** (int_size - 1))
filename = f'uint{int_size}.fits'
uint_hdu.writeto(self.temp(filename))
with fits.open(self.temp(filename), uint=True) as hdul:
new_uint_hdu = hdul[0]
assert np.all(new_uint_hdu.data == arr)
assert new_uint_hdu.data.dtype.name == f'uint{int_size}'
assert 'BZERO' in new_uint_hdu.header
> assert new_uint_hdu.header['BZERO'] == (2 ** (int_size - 1))
pypy/site-packages/astropy/io/fits/tests/test_image.py:677:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ TestImageFunctions.test_uint_header_keywords_removed_after_bitpix_change[False-False] _
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000194b20c8>
from_file = False, do_not_scale = False
@pytest.mark.parametrize(('from_file'), (False, True))
@pytest.mark.parametrize(('do_not_scale'), (False,))
def test_uint_header_keywords_removed_after_bitpix_change(self,
from_file,
do_not_scale):
"""
Regression test for https://github.com/astropy/astropy/issues/4974
BZERO/BSCALE should be removed if data is converted to a floating
point type.
Currently excluding the case where do_not_scale_image_data=True
because it is not clear what the expectation should be.
"""
arr = np.zeros(100, dtype='uint16')
if from_file:
# To generate the proper input file we always want to scale the
# data before writing it...otherwise when we open it will be
# regular (signed) int data.
tmp_uint = fits.PrimaryHDU(arr)
filename = 'unsigned_int.fits'
tmp_uint.writeto(self.temp(filename))
with fits.open(self.temp(filename),
do_not_scale_image_data=do_not_scale) as f:
uint_hdu = f[0]
# Force a read before we close.
_ = uint_hdu.data
else:
uint_hdu = fits.PrimaryHDU(arr,
do_not_scale_image_data=do_not_scale)
# Make sure appropriate keywords are in the header. See
# https://github.com/astropy/astropy/pull/3916#issuecomment-122414532
# for discussion.
assert 'BSCALE' in uint_hdu.header
assert 'BZERO' in uint_hdu.header
assert uint_hdu.header['BSCALE'] == 1
assert uint_hdu.header['BZERO'] == 32768
# Convert data to floating point...
uint_hdu.data = uint_hdu.data * 1.0
# ...bitpix should be negative.
assert uint_hdu.header['BITPIX'] < 0
# BSCALE and BZERO should NOT be in header any more.
assert 'BSCALE' not in uint_hdu.header
assert 'BZERO' not in uint_hdu.header
# This is the main test...the data values should round trip
# as zero.
filename = 'test_uint_to_float.fits'
uint_hdu.writeto(self.temp(filename))
with fits.open(self.temp(filename)) as hdul:
> assert (hdul[0].data == 0).all()
pypy/site-packages/astropy/io/fits/tests/test_image.py:735:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ TestImageFunctions.test_uint_header_keywords_removed_after_bitpix_change[False-True] _
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000016d3c4f0>
from_file = True, do_not_scale = False
@pytest.mark.parametrize(('from_file'), (False, True))
@pytest.mark.parametrize(('do_not_scale'), (False,))
def test_uint_header_keywords_removed_after_bitpix_change(self,
from_file,
do_not_scale):
"""
Regression test for https://github.com/astropy/astropy/issues/4974
BZERO/BSCALE should be removed if data is converted to a floating
point type.
Currently excluding the case where do_not_scale_image_data=True
because it is not clear what the expectation should be.
"""
arr = np.zeros(100, dtype='uint16')
if from_file:
# To generate the proper input file we always want to scale the
# data before writing it...otherwise when we open it will be
# regular (signed) int data.
tmp_uint = fits.PrimaryHDU(arr)
filename = 'unsigned_int.fits'
tmp_uint.writeto(self.temp(filename))
with fits.open(self.temp(filename),
do_not_scale_image_data=do_not_scale) as f:
uint_hdu = f[0]
# Force a read before we close.
> _ = uint_hdu.data
pypy/site-packages/astropy/io/fits/tests/test_image.py:707:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestImageFunctions.test_blanks ________________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000001b1e30f8>
def test_blanks(self):
"""Test image data with blank spots in it (which should show up as
NaNs in the data array.
"""
arr = np.zeros((10, 10), dtype=np.int32)
# One row will be blanks
arr[1] = 999
hdu = fits.ImageHDU(data=arr)
hdu.header['BLANK'] = 999
hdu.writeto(self.temp('test_new.fits'))
with fits.open(self.temp('test_new.fits')) as hdul:
> assert np.isnan(hdul[1].data[1]).all()
pypy/site-packages/astropy/io/fits/tests/test_image.py:750:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestImageFunctions.test_invalid_blanks ____________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000020f43de0>
def test_invalid_blanks(self):
"""
Test that invalid use of the BLANK keyword leads to an appropriate
warning, and that the BLANK keyword is ignored when returning the
HDU data.
Regression test for https://github.com/astropy/astropy/issues/3865
"""
arr = np.arange(5, dtype=np.float64)
hdu = fits.PrimaryHDU(data=arr)
hdu.header['BLANK'] = 2
with catch_warnings() as w:
hdu.writeto(self.temp('test_new.fits'))
# Allow the HDU to be written, but there should be a warning
# when writing a header with BLANK when then data is not
# int
assert len(w) == 1
assert "Invalid 'BLANK' keyword in header" in str(w[0].message)
# Should also get a warning when opening the file, and the BLANK
# value should not be applied
with catch_warnings() as w:
with fits.open(self.temp('test_new.fits')) as h:
assert len(w) == 1
assert "Invalid 'BLANK' keyword in header" in str(w[0].message)
> assert np.all(arr == h[0].data)
pypy/site-packages/astropy/io/fits/tests/test_image.py:779:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestImageFunctions.test_scale_back_with_blanks ________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000001f334678>
def test_scale_back_with_blanks(self):
"""
Test that when auto-rescaling integer data with "blank" values (where
the blanks are replaced by NaN in the float data), that the "BLANK"
keyword is removed from the header.
Further, test that when using the ``scale_back=True`` option the blank
values are restored properly.
Regression test for https://github.com/astropy/astropy/issues/3865
"""
# Make the sample file
arr = np.arange(5, dtype=np.int32)
hdu = fits.PrimaryHDU(data=arr)
hdu.scale('int16', bscale=1.23)
# Creating data that uses BLANK is currently kludgy--a separate issue
# TODO: Rewrite this test when scaling with blank support is better
# supported
# Let's just add a value to the data that should be converted to NaN
# when it is read back in:
filename = self.temp('test.fits')
hdu.data[0] = 9999
hdu.header['BLANK'] = 9999
hdu.writeto(filename)
with fits.open(filename) as hdul:
data = hdul[0].data
assert np.isnan(data[0])
with pytest.warns(fits.verify.VerifyWarning,
match=r"Invalid 'BLANK' keyword in header"):
> hdul.writeto(self.temp('test2.fits'))
pypy/site-packages/astropy/io/fits/tests/test_image.py:814:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestImageFunctions.test_bzero_with_floats ___________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000006a04bf0>
def test_bzero_with_floats(self):
"""Test use of the BZERO keyword in an image HDU containing float
data.
"""
arr = np.zeros((10, 10)) - 1
hdu = fits.ImageHDU(data=arr)
hdu.header['BZERO'] = 1.0
hdu.writeto(self.temp('test_new.fits'))
with fits.open(self.temp('test_new.fits')) as hdul:
arr += 1
> assert (hdul[1].data == arr).all()
pypy/site-packages/astropy/io/fits/tests/test_image.py:849:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestImageFunctions.test_rewriting_large_scaled_image _____________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x000000000f9c29f8>
def test_rewriting_large_scaled_image(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/84 and
https://aeon.stsci.edu/ssb/trac/pyfits/ticket/101
"""
hdul = fits.open(self.data('fixed-1890.fits'))
orig_data = hdul[0].data
with ignore_warnings():
hdul.writeto(self.temp('test_new.fits'), overwrite=True)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:860:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestImageFunctions.test_image_update_header __________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000012455f30>
def test_image_update_header(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/105
Replacing the original header to an image HDU and saving should update
the NAXISn keywords appropriately and save the image data correctly.
"""
# Copy the original file before saving to it
self.copy_file('test0.fits')
with fits.open(self.temp('test0.fits'), mode='update') as hdul:
orig_data = hdul[1].data.copy()
hdr_copy = hdul[1].header.copy()
del hdr_copy['NAXIS*']
> hdul[1].header = hdr_copy
pypy/site-packages/astropy/io/fits/tests/test_image.py:906:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestImageFunctions.test_open_scaled_in_update_mode ______________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000116b4b48>
def test_open_scaled_in_update_mode(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/119
(Don't update scaled image data if the data is not read)
This ensures that merely opening and closing a file containing scaled
image data does not cause any change to the data (or the header).
Changes should only occur if the data is accessed.
"""
# Copy the original file before making any possible changes to it
self.copy_file('scale.fits')
mtime = os.stat(self.temp('scale.fits')).st_mtime
time.sleep(1)
fits.open(self.temp('scale.fits'), mode='update').close()
# Ensure that no changes were made to the file merely by immediately
# opening and closing it.
assert mtime == os.stat(self.temp('scale.fits')).st_mtime
# Insert a slight delay to ensure the mtime does change when the file
# is changed
time.sleep(1)
hdul = fits.open(self.temp('scale.fits'), 'update')
orig_data = hdul[0].data
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_image.py:939:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestImageFunctions.test_scale_back ______________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000113293d0>
def test_scale_back(self):
"""A simple test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/120
The scale_back feature for image HDUs.
"""
self.copy_file('scale.fits')
with fits.open(self.temp('scale.fits'), mode='update',
scale_back=True) as hdul:
orig_bitpix = hdul[0].header['BITPIX']
orig_bzero = hdul[0].header['BZERO']
orig_bscale = hdul[0].header['BSCALE']
orig_data = hdul[0].data.copy()
> hdul[0].data[0] = 0
pypy/site-packages/astropy/io/fits/tests/test_image.py:976:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestImageFunctions.test_image_none ______________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000022367d38>
def test_image_none(self):
"""
Regression test for https://github.com/spacetelescope/PyFITS/issues/27
"""
with fits.open(self.data('test0.fits')) as h:
h[1].data
h[1].data = None
> h[1].writeto(self.temp('test.fits'))
pypy/site-packages/astropy/io/fits/tests/test_image.py:998:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestImageFunctions.test_invalid_blank _____________________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x0000000016c698d8>
def test_invalid_blank(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2711
If the BLANK keyword contains an invalid value it should be ignored for
any calculations (though a warning should be issued).
"""
data = np.arange(100, dtype=np.float64)
hdu = fits.PrimaryHDU(data)
hdu.header['BLANK'] = 'nan'
with pytest.warns(fits.verify.VerifyWarning, match=r"Invalid value for "
r"'BLANK' keyword in header: 'nan'"):
hdu.writeto(self.temp('test.fits'))
with catch_warnings() as w:
with fits.open(self.temp('test.fits')) as hdul:
> assert np.all(hdul[0].data == data)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1023:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestImageFunctions.test_scale_back_uint_assignment ______________
self = <astropy.io.fits.tests.test_image.TestImageFunctions object at 0x00000000149d40c8>
def test_scale_back_uint_assignment(self):
"""
Extend fix for #4600 to assignment to data
Suggested by:
https://github.com/astropy/astropy/pull/4602#issuecomment-208713748
"""
a = np.arange(100, 200, dtype=np.uint16)
fits.PrimaryHDU(a).writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits'), mode="update",
scale_back=True) as (hdu,):
hdu.data[:] = 0
> assert np.allclose(hdu.data, 0)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1086:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestCompressedImage.test_empty ________________________
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000011299168>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000011299088>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
> self.flush(output_verify=output_verify, verbose=verbose)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:963:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = ([<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000011299168>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000011299088>],)
kwargs = {'output_verify': 'exception', 'verbose': False}
curr_thread = <_MainThread(MainThread, started 140018066300352)>
single_thread = True
SigintHandler = <class 'astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler'>
sigint_handler = <astropy.io.fits.util.ignore_sigint.<locals>.wrapped.<locals>.SigintHandler object at 0x00000000112848a8>
old_handler = <built-in function default_int_handler>
@wraps(func)
def wrapped(*args, **kwargs):
# Get the name of the current thread and determine if this is a single
# threaded application
curr_thread = threading.currentThread()
single_thread = (threading.activeCount() == 1 and
curr_thread.getName() == 'MainThread')
class SigintHandler:
def __init__(self):
self.sigint_received = False
def __call__(self, signum, frame):
warnings.warn('KeyboardInterrupt ignored until {} is '
'complete!'.format(func.__name__),
AstropyUserWarning)
self.sigint_received = True
sigint_handler = SigintHandler()
# Define new signal interput handler
if single_thread:
# Install new handler
old_handler = signal.signal(signal.SIGINT, sigint_handler)
try:
> func(*args, **kwargs)
pypy/site-packages/astropy/io/fits/util.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000011299168>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000011299088>]
output_verify = 'exception', verbose = False
@ignore_sigint
def flush(self, output_verify='fix', verbose=False):
"""
Force a write of the `HDUList` back to the file (for append and
update modes only).
Parameters
----------
output_verify : str
Output verification option. Must be one of ``"fix"``,
``"silentfix"``, ``"ignore"``, ``"warn"``, or
``"exception"``. May also be any combination of ``"fix"`` or
``"silentfix"`` with ``"+ignore"``, ``+warn``, or ``+exception"
(e.g. ``"fix+warn"``). See :ref:`verify` for more info.
verbose : bool
When `True`, print verbose messages
"""
if self._file.mode not in ('append', 'update', 'ostream'):
warnings.warn("Flush for '{}' mode is not supported."
.format(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 {} to {}.'.format(
filename, backup), AstropyUserWarning)
try:
shutil.copy(filename, backup)
except OSError as exc:
raise OSError('Failed to save backup to destination {}: '
'{}'.format(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)
with _free_space_check(self):
hdu._writeto(self._file)
if verbose:
print('append HDU', hdu.name, extver)
hdu._new = False
hdu._postwriteto()
elif self._file.mode == 'update':
> self._flush_update()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:842:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000011299168>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000011299088>]
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000011299168>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x0000000011299088>]
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+')
elif self._file.compression == 'bzip2':
if not HAS_BZ2:
raise ModuleNotFoundError(
"This Python installation does not provide the bz2 module.")
new_file = bz2.BZ2File(name, mode='w')
else:
new_file = name
with self.fromfile(new_file, mode='append') as hdulist:
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()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1307:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000011284020>
def test_empty(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2595
"""
hdu = fits.CompImageHDU()
assert hdu.data is None
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits'), mode='update') as hdul:
assert len(hdul) == 2
assert isinstance(hdul[1], fits.CompImageHDU)
assert hdul[1].data is None
# Now test replacing the empty data with an array and see what
# happens
> hdul[1].data = np.arange(100, dtype=np.int32)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1106:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestCompressedImage.test_comp_image[<-data0-RICE_1-16] ____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001d978d08>
data = array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0...],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]], dtype=float32)
compression_type = 'RICE_1', quantize_level = 16, byte_order = '<'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestCompressedImage.test_comp_image[<-data1-GZIP_1--0.01] ___________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00007f587a7874b0>
data = array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0...],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]], dtype=float32)
compression_type = 'GZIP_1', quantize_level = -0.01, byte_order = '<'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestCompressedImage.test_comp_image[<-data2-GZIP_2--0.01] ___________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000ddf4bb8>
data = array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0...],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]], dtype=float32)
compression_type = 'GZIP_2', quantize_level = -0.01, byte_order = '<'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestCompressedImage.test_comp_image[<-data3-HCOMPRESS_1-16] __________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000d20c1e0>
data = array([[1., 1., 1., ..., 1., 1., 1.],
[1., 1., 1., ..., 1., 1., 1.],
[1., 1., 1., ..., 1., 1., 1.],
...,
[1., 1., 1., ..., 1., 1., 1.],
[1., 1., 1., ..., 1., 1., 1.],
[1., 1., 1., ..., 1., 1., 1.]])
compression_type = 'HCOMPRESS_1', quantize_level = 16, byte_order = '<'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestCompressedImage.test_comp_image[<-data4-PLIO_1-16] ____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000012a0d948>
data = array([[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., ...0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
compression_type = 'PLIO_1', quantize_level = 16, byte_order = '<'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestCompressedImage.test_comp_image[>-data0-RICE_1-16] ____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001a0e0f70>
data = array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0...],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]], dtype=float32)
compression_type = 'RICE_1', quantize_level = 16, byte_order = '>'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestCompressedImage.test_comp_image[>-data1-GZIP_1--0.01] ___________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00000000114a5980>
data = array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0...],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]], dtype=float32)
compression_type = 'GZIP_1', quantize_level = -0.01, byte_order = '>'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestCompressedImage.test_comp_image[>-data2-GZIP_2--0.01] ___________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000022361590>
data = array([[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0...],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]], dtype=float32)
compression_type = 'GZIP_2', quantize_level = -0.01, byte_order = '>'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestCompressedImage.test_comp_image[>-data3-HCOMPRESS_1-16] __________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000019c86a30>
data = array([[3.03865e-319, 3.03865e-319, 3.03865e-319, ..., 3.03865e-319,
3.03865e-319, 3.03865e-319],
[3.03...03865e-319],
[3.03865e-319, 3.03865e-319, 3.03865e-319, ..., 3.03865e-319,
3.03865e-319, 3.03865e-319]])
compression_type = 'HCOMPRESS_1', quantize_level = 16, byte_order = '>'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestCompressedImage.test_comp_image[>-data4-PLIO_1-16] ____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001647b210>
data = array([[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., ...0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
compression_type = 'PLIO_1', quantize_level = 16, byte_order = '>'
@pytest.mark.parametrize(
('data', 'compression_type', 'quantize_level'),
[(np.zeros((2, 10, 10), dtype=np.float32), 'RICE_1', 16),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_1', -0.01),
(np.zeros((2, 10, 10), dtype=np.float32), 'GZIP_2', -0.01),
(np.zeros((100, 100)) + 1, 'HCOMPRESS_1', 16),
(np.zeros((10, 10)), 'PLIO_1', 16)])
@pytest.mark.parametrize('byte_order', ['<', '>'])
def test_comp_image(self, data, compression_type, quantize_level,
byte_order):
data = data.newbyteorder(byte_order)
primary_hdu = fits.PrimaryHDU()
ofd = fits.HDUList(primary_hdu)
chdu = fits.CompImageHDU(data, name='SCI',
compression_type=compression_type,
quantize_level=quantize_level)
ofd.append(chdu)
ofd.writeto(self.temp('test_new.fits'), overwrite=True)
ofd.close()
with fits.open(self.temp('test_new.fits')) as fd:
assert (fd[1].data == data).all()
assert fd[1].header['NAXIS'] == chdu.header['NAXIS']
assert fd[1].header['NAXIS1'] == chdu.header['NAXIS1']
assert fd[1].header['NAXIS2'] == chdu.header['NAXIS2']
> assert fd[1].header['BITPIX'] == chdu.header['BITPIX']
pypy/site-packages/astropy/io/fits/tests/test_image.py:1137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestCompressedImage.test_comp_image_hcompress_image_stack ___________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001875d050>
def test_comp_image_hcompress_image_stack(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/171
Tests that data containing more than two dimensions can be
compressed with HCOMPRESS_1 so long as the user-supplied tile size can
be flattened to two dimensions.
"""
cube = np.arange(300, dtype=np.float32).reshape(3, 10, 10)
hdu = fits.CompImageHDU(data=cube, name='SCI',
compression_type='HCOMPRESS_1',
quantize_level=16, tile_size=[5, 5, 1])
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdul:
# HCOMPRESSed images are allowed to deviate from the original by
# about 1/quantize_level of the RMS in each tile.
> assert np.abs(hdul['SCI'].data - cube).max() < 1./15.
pypy/site-packages/astropy/io/fits/tests/test_image.py:1198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestCompressedImage.test_subtractive_dither_seed _______________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000022a339f0>
def test_subtractive_dither_seed(self):
"""
Regression test for https://github.com/spacetelescope/PyFITS/issues/32
Ensure that when floating point data is compressed with the
SUBTRACTIVE_DITHER_1 quantization method that the correct ZDITHER0 seed
is added to the header, and that the data can be correctly
decompressed.
"""
array = np.arange(100.0).reshape(10, 10)
csum = (array[0].view('uint8').sum() % 10000) + 1
hdu = fits.CompImageHDU(data=array,
quantize_method=SUBTRACTIVE_DITHER_1,
dither_seed=DITHER_SEED_CHECKSUM)
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdul:
assert isinstance(hdul[1], fits.CompImageHDU)
assert 'ZQUANTIZ' in hdul[1]._header
assert hdul[1]._header['ZQUANTIZ'] == 'SUBTRACTIVE_DITHER_1'
assert 'ZDITHER0' in hdul[1]._header
assert hdul[1]._header['ZDITHER0'] == csum
> assert np.all(hdul[1].data == array)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1223:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________ TestCompressedImage.test_open_scaled_in_update_mode_compressed ________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000e11ea68>
def test_open_scaled_in_update_mode_compressed(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/88 2
Identical to test_open_scaled_in_update_mode() but with a compressed
version of the scaled image.
"""
# Copy+compress the original file before making any possible changes to
# it
with fits.open(self.data('scale.fits'),
do_not_scale_image_data=True) as hdul:
chdu = fits.CompImageHDU(data=hdul[0].data,
header=hdul[0].header)
> chdu.writeto(self.temp('scale.fits'))
pypy/site-packages/astropy/io/fits/tests/test_image.py:1273:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestCompressedImage.test_write_comp_hdu_direct_from_existing _________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00000000054dea68>
def test_write_comp_hdu_direct_from_existing(self):
with fits.open(self.data('comp.fits')) as hdul:
> hdul[1].writeto(self.temp('test.fits'))
pypy/site-packages/astropy/io/fits/tests/test_image.py:1315:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______ TestCompressedImage.test_rewriting_large_scaled_image_compressed _______
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000c608e90>
def test_rewriting_large_scaled_image_compressed(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/88 1
Identical to test_rewriting_large_scaled_image() but with a compressed
image.
"""
with fits.open(self.data('fixed-1890.fits'),
do_not_scale_image_data=True) as hdul:
chdu = fits.CompImageHDU(data=hdul[0].data,
header=hdul[0].header)
> chdu.writeto(self.temp('fixed-1890-z.fits'))
pypy/site-packages/astropy/io/fits/tests/test_image.py:1335:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestCompressedImage.test_scale_back_compressed ________________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000d29e4b8>
def test_scale_back_compressed(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/88 3
Identical to test_scale_back() but uses a compressed image.
"""
# Create a compressed version of the scaled image
with fits.open(self.data('scale.fits'),
do_not_scale_image_data=True) as hdul:
chdu = fits.CompImageHDU(data=hdul[0].data,
header=hdul[0].header)
> chdu.writeto(self.temp('scale.fits'))
pypy/site-packages/astropy/io/fits/tests/test_image.py:1385:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestCompressedImage.test_lossless_gzip_compression ______________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000f3a58a0>
def test_lossless_gzip_compression(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/198"""
rng = np.random.RandomState(seed=42)
noise = rng.normal(size=(20, 20))
chdu1 = fits.CompImageHDU(data=noise, compression_type='GZIP_1')
# First make a test image with lossy compression and make sure it
# wasn't compressed perfectly. This shouldn't happen ever, but just to
# make sure the test non-trivial.
chdu1.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as h:
> assert np.abs(noise - h[1].data).max() > 0.0
pypy/site-packages/astropy/io/fits/tests/test_image.py:1427:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestCompressedImage.test_compression_with_gzip_column _____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00000000164f50f8>
def test_compression_with_gzip_column(self):
"""
Regression test for https://github.com/spacetelescope/PyFITS/issues/71
"""
arr = np.zeros((2, 7000), dtype='float32')
# The first row (which will be the first compressed tile) has a very
# wide range of values that will be difficult to quantize, and should
# result in use of a GZIP_COMPRESSED_DATA column
arr[0] = np.linspace(0, 1, 7000)
arr[1] = np.random.normal(size=7000)
hdu = fits.CompImageHDU(data=arr)
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdul:
comp_hdu = hdul[1]
# GZIP-compressed tile should compare exactly
> assert np.all(comp_hdu.data[0] == arr[0])
pypy/site-packages/astropy/io/fits/tests/test_image.py:1670:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________ TestCompressedImage.test_scale_back_compressed_uint_assignment ________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00000000189978d8>
def test_scale_back_compressed_uint_assignment(self):
"""
Extend fix for #4600 to assignment to data
Identical to test_scale_back_uint_assignment() but uses a compressed
image.
Suggested by:
https://github.com/astropy/astropy/pull/4602#issuecomment-208713748
"""
a = np.arange(100, 200, dtype=np.uint16)
fits.CompImageHDU(a).writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits'), mode="update",
scale_back=True) as hdul:
hdul[1].data[:] = 0
> assert np.allclose(hdul[1].data, 0)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1733:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____ TestCompressedImage.test_compressed_scaled_float[BSCALE-uint8-float32] ____
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000c519b08>
keyword = 'BSCALE', dtype = <class 'numpy.uint8'>
expected = <class 'numpy.float32'>
@pytest.mark.parametrize(
('keyword', 'dtype', 'expected'),
[('BSCALE', np.uint8, np.float32), ('BSCALE', np.int16, np.float32),
('BSCALE', np.int32, np.float64), ('BZERO', np.uint8, np.float32),
('BZERO', np.int16, np.float32), ('BZERO', np.int32, np.float64)])
def test_compressed_scaled_float(self, keyword, dtype, expected):
"""
If BSCALE,BZERO is set to floating point values, the image
should be floating-point.
https://github.com/astropy/astropy/pull/6492
Parameters
----------
keyword : `str`
Keyword to set to a floating-point value to trigger
floating-point pixels.
dtype : `numpy.dtype`
Type of original array.
expected : `numpy.dtype`
Expected type of uncompressed array.
"""
value = 1.23345 # A floating-point value
hdu = fits.CompImageHDU(np.arange(0, 10, dtype=dtype))
hdu.header[keyword] = value
hdu.writeto(self.temp('test.fits'))
del hdu
with fits.open(self.temp('test.fits')) as hdu:
assert hdu[1].header[keyword] == value
> assert hdu[1].data.dtype == expected
pypy/site-packages/astropy/io/fits/tests/test_image.py:1775:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____ TestCompressedImage.test_compressed_scaled_float[BSCALE-int16-float32] ____
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000008cff398>
keyword = 'BSCALE', dtype = <class 'numpy.int16'>
expected = <class 'numpy.float32'>
@pytest.mark.parametrize(
('keyword', 'dtype', 'expected'),
[('BSCALE', np.uint8, np.float32), ('BSCALE', np.int16, np.float32),
('BSCALE', np.int32, np.float64), ('BZERO', np.uint8, np.float32),
('BZERO', np.int16, np.float32), ('BZERO', np.int32, np.float64)])
def test_compressed_scaled_float(self, keyword, dtype, expected):
"""
If BSCALE,BZERO is set to floating point values, the image
should be floating-point.
https://github.com/astropy/astropy/pull/6492
Parameters
----------
keyword : `str`
Keyword to set to a floating-point value to trigger
floating-point pixels.
dtype : `numpy.dtype`
Type of original array.
expected : `numpy.dtype`
Expected type of uncompressed array.
"""
value = 1.23345 # A floating-point value
hdu = fits.CompImageHDU(np.arange(0, 10, dtype=dtype))
hdu.header[keyword] = value
hdu.writeto(self.temp('test.fits'))
del hdu
with fits.open(self.temp('test.fits')) as hdu:
assert hdu[1].header[keyword] == value
> assert hdu[1].data.dtype == expected
pypy/site-packages/astropy/io/fits/tests/test_image.py:1775:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____ TestCompressedImage.test_compressed_scaled_float[BSCALE-int32-float64] ____
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000000cf32720>
keyword = 'BSCALE', dtype = <class 'numpy.int32'>
expected = <class 'numpy.float64'>
@pytest.mark.parametrize(
('keyword', 'dtype', 'expected'),
[('BSCALE', np.uint8, np.float32), ('BSCALE', np.int16, np.float32),
('BSCALE', np.int32, np.float64), ('BZERO', np.uint8, np.float32),
('BZERO', np.int16, np.float32), ('BZERO', np.int32, np.float64)])
def test_compressed_scaled_float(self, keyword, dtype, expected):
"""
If BSCALE,BZERO is set to floating point values, the image
should be floating-point.
https://github.com/astropy/astropy/pull/6492
Parameters
----------
keyword : `str`
Keyword to set to a floating-point value to trigger
floating-point pixels.
dtype : `numpy.dtype`
Type of original array.
expected : `numpy.dtype`
Expected type of uncompressed array.
"""
value = 1.23345 # A floating-point value
hdu = fits.CompImageHDU(np.arange(0, 10, dtype=dtype))
hdu.header[keyword] = value
hdu.writeto(self.temp('test.fits'))
del hdu
with fits.open(self.temp('test.fits')) as hdu:
assert hdu[1].header[keyword] == value
> assert hdu[1].data.dtype == expected
pypy/site-packages/astropy/io/fits/tests/test_image.py:1775:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____ TestCompressedImage.test_compressed_scaled_float[BZERO-uint8-float32] _____
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000013ded168>
keyword = 'BZERO', dtype = <class 'numpy.uint8'>
expected = <class 'numpy.float32'>
@pytest.mark.parametrize(
('keyword', 'dtype', 'expected'),
[('BSCALE', np.uint8, np.float32), ('BSCALE', np.int16, np.float32),
('BSCALE', np.int32, np.float64), ('BZERO', np.uint8, np.float32),
('BZERO', np.int16, np.float32), ('BZERO', np.int32, np.float64)])
def test_compressed_scaled_float(self, keyword, dtype, expected):
"""
If BSCALE,BZERO is set to floating point values, the image
should be floating-point.
https://github.com/astropy/astropy/pull/6492
Parameters
----------
keyword : `str`
Keyword to set to a floating-point value to trigger
floating-point pixels.
dtype : `numpy.dtype`
Type of original array.
expected : `numpy.dtype`
Expected type of uncompressed array.
"""
value = 1.23345 # A floating-point value
hdu = fits.CompImageHDU(np.arange(0, 10, dtype=dtype))
hdu.header[keyword] = value
hdu.writeto(self.temp('test.fits'))
del hdu
with fits.open(self.temp('test.fits')) as hdu:
assert hdu[1].header[keyword] == value
> assert hdu[1].data.dtype == expected
pypy/site-packages/astropy/io/fits/tests/test_image.py:1775:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____ TestCompressedImage.test_compressed_scaled_float[BZERO-int16-float32] _____
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001696a918>
keyword = 'BZERO', dtype = <class 'numpy.int16'>
expected = <class 'numpy.float32'>
@pytest.mark.parametrize(
('keyword', 'dtype', 'expected'),
[('BSCALE', np.uint8, np.float32), ('BSCALE', np.int16, np.float32),
('BSCALE', np.int32, np.float64), ('BZERO', np.uint8, np.float32),
('BZERO', np.int16, np.float32), ('BZERO', np.int32, np.float64)])
def test_compressed_scaled_float(self, keyword, dtype, expected):
"""
If BSCALE,BZERO is set to floating point values, the image
should be floating-point.
https://github.com/astropy/astropy/pull/6492
Parameters
----------
keyword : `str`
Keyword to set to a floating-point value to trigger
floating-point pixels.
dtype : `numpy.dtype`
Type of original array.
expected : `numpy.dtype`
Expected type of uncompressed array.
"""
value = 1.23345 # A floating-point value
hdu = fits.CompImageHDU(np.arange(0, 10, dtype=dtype))
hdu.header[keyword] = value
hdu.writeto(self.temp('test.fits'))
del hdu
with fits.open(self.temp('test.fits')) as hdu:
assert hdu[1].header[keyword] == value
> assert hdu[1].data.dtype == expected
pypy/site-packages/astropy/io/fits/tests/test_image.py:1775:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____ TestCompressedImage.test_compressed_scaled_float[BZERO-int32-float64] _____
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00000000185de560>
keyword = 'BZERO', dtype = <class 'numpy.int32'>
expected = <class 'numpy.float64'>
@pytest.mark.parametrize(
('keyword', 'dtype', 'expected'),
[('BSCALE', np.uint8, np.float32), ('BSCALE', np.int16, np.float32),
('BSCALE', np.int32, np.float64), ('BZERO', np.uint8, np.float32),
('BZERO', np.int16, np.float32), ('BZERO', np.int32, np.float64)])
def test_compressed_scaled_float(self, keyword, dtype, expected):
"""
If BSCALE,BZERO is set to floating point values, the image
should be floating-point.
https://github.com/astropy/astropy/pull/6492
Parameters
----------
keyword : `str`
Keyword to set to a floating-point value to trigger
floating-point pixels.
dtype : `numpy.dtype`
Type of original array.
expected : `numpy.dtype`
Expected type of uncompressed array.
"""
value = 1.23345 # A floating-point value
hdu = fits.CompImageHDU(np.arange(0, 10, dtype=dtype))
hdu.header[keyword] = value
hdu.writeto(self.temp('test.fits'))
del hdu
with fits.open(self.temp('test.fits')) as hdu:
assert hdu[1].header[keyword] == value
> assert hdu[1].data.dtype == expected
pypy/site-packages/astropy/io/fits/tests/test_image.py:1775:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestCompressedImage.test_compressed_integers[uint8] ______________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000018a56448>
dtype = <class 'numpy.uint8'>
@pytest.mark.parametrize('dtype', (np.uint8, np.int16, np.uint16, np.int32,
np.uint32))
def test_compressed_integers(self, dtype):
"""Test that the various integer dtypes are correctly written and read.
Regression test for https://github.com/astropy/astropy/issues/9072
"""
mid = np.iinfo(dtype).max // 2
data = np.arange(mid-50, mid+50, dtype=dtype)
testfile = self.temp('test.fits')
hdu = fits.CompImageHDU(data=data)
hdu.writeto(testfile, overwrite=True)
> new = fits.getdata(testfile)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1790:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestCompressedImage.test_compressed_integers[int16] ______________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001c2574b0>
dtype = <class 'numpy.int16'>
@pytest.mark.parametrize('dtype', (np.uint8, np.int16, np.uint16, np.int32,
np.uint32))
def test_compressed_integers(self, dtype):
"""Test that the various integer dtypes are correctly written and read.
Regression test for https://github.com/astropy/astropy/issues/9072
"""
mid = np.iinfo(dtype).max // 2
data = np.arange(mid-50, mid+50, dtype=dtype)
testfile = self.temp('test.fits')
hdu = fits.CompImageHDU(data=data)
hdu.writeto(testfile, overwrite=True)
> new = fits.getdata(testfile)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1790:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestCompressedImage.test_compressed_integers[uint16] _____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x00000000133c8138>
dtype = <class 'numpy.uint16'>
@pytest.mark.parametrize('dtype', (np.uint8, np.int16, np.uint16, np.int32,
np.uint32))
def test_compressed_integers(self, dtype):
"""Test that the various integer dtypes are correctly written and read.
Regression test for https://github.com/astropy/astropy/issues/9072
"""
mid = np.iinfo(dtype).max // 2
data = np.arange(mid-50, mid+50, dtype=dtype)
testfile = self.temp('test.fits')
hdu = fits.CompImageHDU(data=data)
hdu.writeto(testfile, overwrite=True)
> new = fits.getdata(testfile)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1790:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestCompressedImage.test_compressed_integers[int32] ______________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x0000000011338288>
dtype = <class 'numpy.int32'>
@pytest.mark.parametrize('dtype', (np.uint8, np.int16, np.uint16, np.int32,
np.uint32))
def test_compressed_integers(self, dtype):
"""Test that the various integer dtypes are correctly written and read.
Regression test for https://github.com/astropy/astropy/issues/9072
"""
mid = np.iinfo(dtype).max // 2
data = np.arange(mid-50, mid+50, dtype=dtype)
testfile = self.temp('test.fits')
hdu = fits.CompImageHDU(data=data)
hdu.writeto(testfile, overwrite=True)
> new = fits.getdata(testfile)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1790:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestCompressedImage.test_compressed_integers[uint32] _____________
self = <astropy.io.fits.tests.test_image.TestCompressedImage object at 0x000000001aead088>
dtype = <class 'numpy.uint32'>
@pytest.mark.parametrize('dtype', (np.uint8, np.int16, np.uint16, np.int32,
np.uint32))
def test_compressed_integers(self, dtype):
"""Test that the various integer dtypes are correctly written and read.
Regression test for https://github.com/astropy/astropy/issues/9072
"""
mid = np.iinfo(dtype).max // 2
data = np.arange(mid-50, mid+50, dtype=dtype)
testfile = self.temp('test.fits')
hdu = fits.CompImageHDU(data=data)
hdu.writeto(testfile, overwrite=True)
> new = fits.getdata(testfile)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1790:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________________ test_comphdu_bscale ______________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_comphdu_bscale0')
def test_comphdu_bscale(tmpdir):
"""
Regression test for a bug that caused extensions that used BZERO and BSCALE
that got turned into CompImageHDU to end up with BZERO/BSCALE before the
TFIELDS.
"""
filename1 = tmpdir.join('3hdus.fits').strpath
filename2 = tmpdir.join('3hdus_comp.fits').strpath
x = np.random.random((100, 100))*100
x0 = fits.PrimaryHDU()
x1 = fits.ImageHDU(np.array(x-50, dtype=int), uint=True)
x1.header['BZERO'] = 20331
x1.header['BSCALE'] = 2.3
hdus = fits.HDUList([x0, x1])
hdus.writeto(filename1)
# fitsverify (based on cfitsio) should fail on this file, only seeing the
# first HDU.
with fits.open(filename1) as hdus:
hdus[1] = fits.CompImageHDU(data=hdus[1].data.astype(np.uint32),
header=hdus[1].header)
> hdus.writeto(filename2)
pypy/site-packages/astropy/io/fits/tests/test_image.py:1818:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ test_bzero_implicit_casting_compressed ____________________
def test_bzero_implicit_casting_compressed():
# Regression test for an issue that occurred because Numpy now does not
# allow implicit type casting during inplace operations. Astropy is
# actually not able to produce a file that triggers the failure - the
# issue occurs when using unsigned integer types in the FITS file, in which
# case BZERO should be 32768. But if the keyword is stored as 32768.0, then
# it was possible to trigger the implicit casting error.
filename = os.path.join(os.path.dirname(__file__),
'data', 'compressed_float_bzero.fits')
with fits.open(filename) as hdul:
hdu = hdul[1]
> hdu.data
pypy/site-packages/astropy/io/fits/tests/test_image.py:1848:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________________ test_image_write_readonly ___________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_image_write_readonly0')
def test_image_write_readonly(tmpdir):
# Regression test to make sure that we can write out read-only arrays (#5512)
x = np.array([1, 2, 3])
x.setflags(write=False)
ghdu = fits.ImageHDU(data=x)
ghdu.add_datasum()
filename = tmpdir.join('test.fits').strpath
ghdu.writeto(filename)
with fits.open(filename) as hdulist:
> assert_equal(hdulist[1].data, [1, 2, 3])
pypy/site-packages/astropy/io/fits/tests/test_image.py:1878:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestNonstandardHdus.test_create_fitshdu ____________________
self = <astropy.io.fits.tests.test_nonstandard.TestNonstandardHdus object at 0x0000000010228ad8>
def test_create_fitshdu(self):
"""
A round trip test of creating a FitsHDU, adding a FITS file to it,
writing the FitsHDU out as part of a new FITS file, and then reading
it and recovering the original FITS file.
"""
> self._test_create_fitshdu(compression=False)
pypy/site-packages/astropy/io/fits/tests/test_nonstandard.py:17:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_nonstandard.py:68: in _test_create_fitshdu
hdul_orig.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________ TestNonstandardHdus.test_create_fitshdu_with_compression ___________
self = <astropy.io.fits.tests.test_nonstandard.TestNonstandardHdus object at 0x000000000cc663a0>
def test_create_fitshdu_with_compression(self):
"""Same as test_create_fitshdu but with gzip compression enabled."""
> self._test_create_fitshdu(compression=True)
pypy/site-packages/astropy/io/fits/tests/test_nonstandard.py:22:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_nonstandard.py:68: in _test_create_fitshdu
hdul_orig.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestNonstandardHdus.test_create_fitshdu_from_filename _____________
self = <astropy.io.fits.tests.test_nonstandard.TestNonstandardHdus object at 0x000000000df9ec60>
def test_create_fitshdu_from_filename(self):
"""Regression test on `FitsHDU.fromfile`"""
# Build up a simple test FITS file
a = np.arange(100)
phdu = fits.PrimaryHDU(data=a)
phdu.header['TEST1'] = 'A'
phdu.header['TEST2'] = 'B'
imghdu = fits.ImageHDU(data=a + 1)
phdu.header['TEST3'] = 'C'
phdu.header['TEST4'] = 'D'
hdul = fits.HDUList([phdu, imghdu])
hdul.writeto(self.temp('test.fits'))
> fitshdu = fits.FitsHDU.fromfile(self.temp('test.fits'))
pypy/site-packages/astropy/io/fits/tests/test_nonstandard.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/nonstandard.py:56: in fromfile
return cls.fromhdulist(hdulist, compress=compress)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestStructured.test_structured ________________________
self = <astropy.io.fits.tests.test_structured.TestStructured object at 0x000000000d793910>
def test_structured(self):
fname = self.data('stddata.fits')
> data1, h1 = fits.getdata(fname, ext=1, header=True)
pypy/site-packages/astropy/io/fits/tests/test_structured.py:77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________________ TestTableFunctions.test_open _________________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000e069e88>
def test_open(self):
# open some existing FITS files:
tt = fits.open(self.data('tb.fits'))
fd = fits.open(self.data('test0.fits'))
# create some local arrays
a1 = chararray.array(['abc', 'def', 'xx'])
r1 = np.array([11., 12., 13.], dtype=np.float32)
# create a table from scratch, using a mixture of columns from existing
# tables and locally created arrays:
# first, create individual column definitions
c1 = fits.Column(name='abc', format='3A', array=a1)
c2 = fits.Column(name='def', format='E', array=r1)
a3 = np.array([3, 4, 5], dtype='i2')
c3 = fits.Column(name='xyz', format='I', array=a3)
a4 = np.array([1, 2, 3], dtype='i2')
c4 = fits.Column(name='t1', format='I', array=a4)
a5 = np.array([3 + 3j, 4 + 4j, 5 + 5j], dtype='c8')
c5 = fits.Column(name='t2', format='C', array=a5)
# Note that X format must be two-D array
a6 = np.array([[0], [1], [0]], dtype=np.uint8)
c6 = fits.Column(name='t3', format='X', array=a6)
a7 = np.array([101, 102, 103], dtype='i4')
c7 = fits.Column(name='t4', format='J', array=a7)
a8 = np.array([[1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1],
[0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0],
[1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1]], dtype=np.uint8)
c8 = fits.Column(name='t5', format='11X', array=a8)
# second, create a column-definitions object for all columns in a table
x = fits.ColDefs([c1, c2, c3, c4, c5, c6, c7, c8])
tbhdu = fits.BinTableHDU.from_columns(x)
# another way to create a table is by using existing table's
# information:
x2 = fits.ColDefs(tt[1])
t2 = fits.BinTableHDU.from_columns(x2, nrows=2)
ra = np.rec.array([
(1, 'abc', 3.7000002861022949, 0),
(2, 'xy ', 6.6999998092651367, 1)], names='c1, c2, c3, c4')
assert comparerecords(t2.data, ra)
# the table HDU's data is a subclass of a record array, so we can
# access one row like this:
assert tbhdu.data[1][0] == a1[1]
assert tbhdu.data[1][1] == r1[1]
assert tbhdu.data[1][2] == a3[1]
assert tbhdu.data[1][3] == a4[1]
assert tbhdu.data[1][4] == a5[1]
assert (tbhdu.data[1][5] == a6[1].view('bool')).all()
assert tbhdu.data[1][6] == a7[1]
assert (tbhdu.data[1][7] == a8[1]).all()
# and a column like this:
assert str(tbhdu.data.field('abc')) == "['abc' 'def' 'xx']"
# An alternative way to create a column-definitions object is from an
# existing table.
_ = fits.ColDefs(tt[1])
# now we write out the newly created table HDU to a FITS file:
fout = fits.HDUList(fits.PrimaryHDU())
fout.append(tbhdu)
fout.writeto(self.temp('tableout1.fits'), overwrite=True)
with fits.open(self.temp('tableout1.fits')) as f2:
temp = f2[1].data.field(7)
> assert (temp[0] == [True, True, False, True, False, True,
True, True, False, False, True]).all()
pypy/site-packages/astropy/io/fits/tests/test_table.py:205:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestTableFunctions.test_binary_table _____________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000018d30368>
def test_binary_table(self):
# binary table:
t = fits.open(self.data('tb.fits'))
assert t[1].header['tform1'] == '1J'
info = {'name': ['c1', 'c2', 'c3', 'c4'],
'format': ['1J', '3A', '1E', '1L'],
'unit': ['', '', '', ''],
'null': [-2147483647, '', '', ''],
'bscale': ['', '', 3, ''],
'bzero': ['', '', 0.4, ''],
'disp': ['I11', 'A3', 'G15.7', 'L6'],
'start': ['', '', '', ''],
'dim': ['', '', '', ''],
'coord_inc': ['', '', '', ''],
'coord_type': ['', '', '', ''],
'coord_unit': ['', '', '', ''],
'coord_ref_point': ['', '', '', ''],
'coord_ref_value': ['', '', '', ''],
'time_ref_pos': ['', '', '', '']}
assert t[1].columns.info(output=False) == info
ra = np.rec.array([
(1, 'abc', 3.7000002861022949, 0),
(2, 'xy ', 6.6999998092651367, 1)], names='c1, c2, c3, c4')
assert comparerecords(t[1].data, ra[:2])
# Change scaled field and scale back to the original array
t[1].data.field('c4')[0] = 1
t[1].data._scale_back()
assert str(np.rec.recarray.field(t[1].data, 'c4')) == '[84 84]'
# look at data column-wise
assert (t[1].data.field(0) == np.array([1, 2])).all()
# When there are scaled columns, the raw data are in data._parent
> t.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:255:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestTableFunctions.test_ascii_table ______________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001908d6e0>
def test_ascii_table(self):
# ASCII table
a = fits.open(self.data('ascii.fits'))
ra1 = np.rec.array([
(10.123000144958496, 37),
(5.1999998092651367, 23),
(15.609999656677246, 17),
(0.0, 0),
(345.0, 345)], names='c1, c2')
assert comparerecords(a[1].data, ra1)
# Test slicing
a2 = a[1].data[2:][2:]
ra2 = np.rec.array([(345.0, 345)], names='c1, c2')
assert comparerecords(a2, ra2)
assert (a2.field(1) == np.array([345])).all()
ra3 = np.rec.array([
(10.123000144958496, 37),
(15.609999656677246, 17),
(345.0, 345)
], names='c1, c2')
assert comparerecords(a[1].data[::2], ra3)
# Test Start Column
a1 = chararray.array(['abcd', 'def'])
r1 = np.array([11., 12.])
c1 = fits.Column(name='abc', format='A3', start=19, array=a1)
c2 = fits.Column(name='def', format='E', start=3, array=r1)
c3 = fits.Column(name='t1', format='I', array=[91, 92, 93])
hdu = fits.TableHDU.from_columns([c2, c1, c3])
assert (dict(hdu.data.dtype.fields) ==
{'abc': (np.dtype('|S3'), 18),
'def': (np.dtype('|S15'), 2),
't1': (np.dtype('|S10'), 21)})
hdu.writeto(self.temp('toto.fits'), overwrite=True)
hdul = fits.open(self.temp('toto.fits'))
assert comparerecords(hdu.data, hdul[1].data)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:300:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestTableFunctions.test_endianness ______________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000022b9e950>
def test_endianness(self):
x = np.ndarray((1,), dtype=object)
channelsIn = np.array([3], dtype='uint8')
x[0] = channelsIn
col = fits.Column(name="Channels", format="PB()", array=x)
cols = fits.ColDefs([col])
tbhdu = fits.BinTableHDU.from_columns(cols)
tbhdu.name = "RFI"
tbhdu.writeto(self.temp('testendian.fits'), overwrite=True)
hduL = fits.open(self.temp('testendian.fits'))
rfiHDU = hduL['RFI']
data = rfiHDU.data
channelsOut = data.field('Channels')[0]
assert (channelsIn == channelsOut).all()
> hduL.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:330:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestTableFunctions.test_column_endianness ___________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001241fde0>
def test_column_endianness(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/77
(Astropy doesn't preserve byte order of non-native order column arrays)
"""
a = [1., 2., 3., 4.]
a1 = np.array(a, dtype='<f8')
a2 = np.array(a, dtype='>f8')
col1 = fits.Column(name='a', format='D', array=a1)
col2 = fits.Column(name='b', format='D', array=a2)
cols = fits.ColDefs([col1, col2])
tbhdu = fits.BinTableHDU.from_columns(cols)
assert (tbhdu.data['a'] == a1).all()
assert (tbhdu.data['b'] == a2).all()
# Double check that the array is converted to the correct byte-order
# for FITS (big-endian).
tbhdu.writeto(self.temp('testendian.fits'), overwrite=True)
with fits.open(self.temp('testendian.fits')) as hdul:
assert (hdul[1].data['a'] == a2).all()
> assert (hdul[1].data['b'] == a2).all()
pypy/site-packages/astropy/io/fits/tests/test_table.py:355:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestTableFunctions.test_recarray_to_bintablehdu ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000013364330>
def test_recarray_to_bintablehdu(self):
bright = np.rec.array(
[(1, 'Serius', -1.45, 'A1V'),
(2, 'Canopys', -0.73, 'F0Ib'),
(3, 'Rigil Kent', -0.1, 'G2V')],
formats='int16,a20,float32,a10',
names='order,name,mag,Sp')
hdu = fits.BinTableHDU(bright)
assert comparerecords(hdu.data, bright)
hdu.writeto(self.temp('toto.fits'), overwrite=True)
hdul = fits.open(self.temp('toto.fits'))
assert comparerecords(hdu.data, hdul[1].data)
assert comparerecords(bright, hdul[1].data)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:370:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestTableFunctions.test_numpy_ndarray_to_bintablehdu _____________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000019a7ae20>
def test_numpy_ndarray_to_bintablehdu(self):
desc = np.dtype({'names': ['order', 'name', 'mag', 'Sp'],
'formats': ['int', 'S20', 'float32', 'S10']})
a = np.array([(1, 'Serius', -1.45, 'A1V'),
(2, 'Canopys', -0.73, 'F0Ib'),
(3, 'Rigil Kent', -0.1, 'G2V')], dtype=desc)
hdu = fits.BinTableHDU(a)
assert comparerecords(hdu.data, a.view(fits.FITS_rec))
hdu.writeto(self.temp('toto.fits'), overwrite=True)
hdul = fits.open(self.temp('toto.fits'))
assert comparerecords(hdu.data, hdul[1].data)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:383:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______ TestTableFunctions.test_numpy_ndarray_to_bintablehdu_with_unicode _______
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000d2b3ec0>
def test_numpy_ndarray_to_bintablehdu_with_unicode(self):
desc = np.dtype({'names': ['order', 'name', 'mag', 'Sp'],
'formats': ['int', 'U20', 'float32', 'U10']})
a = np.array([(1, 'Serius', -1.45, 'A1V'),
(2, 'Canopys', -0.73, 'F0Ib'),
(3, 'Rigil Kent', -0.1, 'G2V')], dtype=desc)
hdu = fits.BinTableHDU(a)
assert comparerecords(hdu.data, a.view(fits.FITS_rec))
hdu.writeto(self.temp('toto.fits'), overwrite=True)
hdul = fits.open(self.temp('toto.fits'))
assert comparerecords(hdu.data, hdul[1].data)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:396:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestTableFunctions.test_new_table_from_recarray ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000dba8090>
def test_new_table_from_recarray(self):
bright = np.rec.array([(1, 'Serius', -1.45, 'A1V'),
(2, 'Canopys', -0.73, 'F0Ib'),
(3, 'Rigil Kent', -0.1, 'G2V')],
formats='int16,a20,float64,a10',
names='order,name,mag,Sp')
hdu = fits.TableHDU.from_columns(bright, nrows=2)
# Verify that all ndarray objects within the HDU reference the
# same ndarray.
assert (id(hdu.data._coldefs.columns[0].array) ==
id(hdu.data._coldefs._arrays[0]))
assert (id(hdu.data._coldefs.columns[0].array) ==
id(hdu.columns.columns[0].array))
assert (id(hdu.data._coldefs.columns[0].array) ==
id(hdu.columns._arrays[0]))
# Ensure I can change the value of one data element and it effects
# all of the others.
hdu.data[0][0] = 213
assert hdu.data[0][0] == 213
assert hdu.data._coldefs._arrays[0][0] == 213
assert hdu.data._coldefs.columns[0].array[0] == 213
assert hdu.columns._arrays[0][0] == 213
assert hdu.columns.columns[0].array[0] == 213
hdu.data._coldefs._arrays[0][0] = 100
assert hdu.data[0][0] == 100
assert hdu.data._coldefs._arrays[0][0] == 100
assert hdu.data._coldefs.columns[0].array[0] == 100
assert hdu.columns._arrays[0][0] == 100
assert hdu.columns.columns[0].array[0] == 100
hdu.data._coldefs.columns[0].array[0] = 500
assert hdu.data[0][0] == 500
assert hdu.data._coldefs._arrays[0][0] == 500
assert hdu.data._coldefs.columns[0].array[0] == 500
assert hdu.columns._arrays[0][0] == 500
assert hdu.columns.columns[0].array[0] == 500
hdu.columns._arrays[0][0] = 600
assert hdu.data[0][0] == 600
assert hdu.data._coldefs._arrays[0][0] == 600
assert hdu.data._coldefs.columns[0].array[0] == 600
assert hdu.columns._arrays[0][0] == 600
assert hdu.columns.columns[0].array[0] == 600
hdu.columns.columns[0].array[0] = 800
assert hdu.data[0][0] == 800
assert hdu.data._coldefs._arrays[0][0] == 800
assert hdu.data._coldefs.columns[0].array[0] == 800
assert hdu.columns._arrays[0][0] == 800
assert hdu.columns.columns[0].array[0] == 800
assert (hdu.data.field(0) ==
np.array([800, 2], dtype=np.int16)).all()
assert hdu.data[0][1] == 'Serius'
assert hdu.data[1][1] == 'Canopys'
assert (hdu.data.field(2) ==
np.array([-1.45, -0.73], dtype=np.float64)).all()
assert hdu.data[0][3] == 'A1V'
assert hdu.data[1][3] == 'F0Ib'
with ignore_warnings():
hdu.writeto(self.temp('toto.fits'), overwrite=True)
with fits.open(self.temp('toto.fits')) as hdul:
assert (hdul[1].data.field(0) ==
np.array([800, 2], dtype=np.int16)).all()
assert hdul[1].data[0][1] == 'Serius'
assert hdul[1].data[1][1] == 'Canopys'
assert (hdul[1].data.field(2) ==
np.array([-1.45, -0.73], dtype=np.float64)).all()
assert hdul[1].data[0][3] == 'A1V'
> assert hdul[1].data[1][3] == 'F0Ib'
pypy/site-packages/astropy/io/fits/tests/test_table.py:474:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestTableFunctions.test_new_fitsrec ______________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000d5d26e8>
def test_new_fitsrec(self):
"""
Tests creating a new FITS_rec object from a multi-field ndarray.
"""
with fits.open(self.data('tb.fits')) as h:
> data = h[1].data
pypy/site-packages/astropy/io/fits/tests/test_table.py:494:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestTableFunctions.test_appending_a_column __________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000f2051a0>
def test_appending_a_column(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.writeto(self.temp('table1.fits'))
counts = np.array([412, 434, 408, 417])
names = np.array(['NGC5', 'NGC6', 'NGC7', 'NCG8'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[0, 1, 0, 0])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.writeto(self.temp('table2.fits'))
# Append the rows of table 2 after the rows of table 1
# The column definitions are assumed to be the same
# Open the two files we want to append
t1 = fits.open(self.temp('table1.fits'))
t2 = fits.open(self.temp('table2.fits'))
# Get the number of rows in the table from the first file
nrows1 = t1[1].data.shape[0]
# Get the total number of rows in the resulting appended table
nrows = t1[1].data.shape[0] + t2[1].data.shape[0]
assert (t1[1].columns._arrays[1] is t1[1].columns.columns[1].array)
# Create a new table that consists of the data from the first table
# but has enough space in the ndarray to hold the data from both tables
hdu = fits.BinTableHDU.from_columns(t1[1].columns, nrows=nrows)
# For each column in the tables append the data from table 2 after the
# data from table 1.
for i in range(len(t1[1].columns)):
hdu.data.field(i)[nrows1:] = t2[1].data.field(i)
hdu.writeto(self.temp('newtable.fits'))
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 4, (), '', ''),
(1, '', 1, 'BinTableHDU', 19, '8R x 5C', '[10A, J, 10A, 5E, L]',
'')]
assert fits.info(self.temp('newtable.fits'), output=False) == info
z = np.array([0., 0., 0., 0., 0.], dtype=np.float32)
array = np.rec.array(
[('NGC1', 312, '', z, True),
('NGC2', 334, '', z, False),
('NGC3', 308, '', z, True),
('NCG4', 317, '', z, True),
('NGC5', 412, '', z, False),
('NGC6', 434, '', z, True),
('NGC7', 408, '', z, False),
('NCG8', 417, '', z, False)],
formats='a10,u4,a10,5f4,l')
assert comparerecords(hdu.data, array)
# Verify that all of the references to the data point to the same
# numarray
hdu.data[0][1] = 300
assert hdu.data._coldefs._arrays[1][0] == 300
assert hdu.data._coldefs.columns[1].array[0] == 300
assert hdu.columns._arrays[1][0] == 300
assert hdu.columns.columns[1].array[0] == 300
assert hdu.data[0][1] == 300
hdu.data._coldefs._arrays[1][0] = 200
assert hdu.data._coldefs._arrays[1][0] == 200
assert hdu.data._coldefs.columns[1].array[0] == 200
assert hdu.columns._arrays[1][0] == 200
assert hdu.columns.columns[1].array[0] == 200
assert hdu.data[0][1] == 200
hdu.data._coldefs.columns[1].array[0] = 100
assert hdu.data._coldefs._arrays[1][0] == 100
assert hdu.data._coldefs.columns[1].array[0] == 100
assert hdu.columns._arrays[1][0] == 100
assert hdu.columns.columns[1].array[0] == 100
assert hdu.data[0][1] == 100
hdu.columns._arrays[1][0] = 90
assert hdu.data._coldefs._arrays[1][0] == 90
assert hdu.data._coldefs.columns[1].array[0] == 90
assert hdu.columns._arrays[1][0] == 90
assert hdu.columns.columns[1].array[0] == 90
assert hdu.data[0][1] == 90
hdu.columns.columns[1].array[0] = 80
assert hdu.data._coldefs._arrays[1][0] == 80
assert hdu.data._coldefs.columns[1].array[0] == 80
assert hdu.columns._arrays[1][0] == 80
assert hdu.columns.columns[1].array[0] == 80
assert hdu.data[0][1] == 80
# Same verification from the file
hdul = fits.open(self.temp('newtable.fits'))
hdu = hdul[1]
hdu.data[0][1] = 300
assert hdu.data._coldefs._arrays[1][0] == 300
assert hdu.data._coldefs.columns[1].array[0] == 300
assert hdu.columns._arrays[1][0] == 300
assert hdu.columns.columns[1].array[0] == 300
assert hdu.data[0][1] == 300
hdu.data._coldefs._arrays[1][0] = 200
assert hdu.data._coldefs._arrays[1][0] == 200
assert hdu.data._coldefs.columns[1].array[0] == 200
assert hdu.columns._arrays[1][0] == 200
assert hdu.columns.columns[1].array[0] == 200
assert hdu.data[0][1] == 200
hdu.data._coldefs.columns[1].array[0] = 100
assert hdu.data._coldefs._arrays[1][0] == 100
assert hdu.data._coldefs.columns[1].array[0] == 100
assert hdu.columns._arrays[1][0] == 100
assert hdu.columns.columns[1].array[0] == 100
assert hdu.data[0][1] == 100
hdu.columns._arrays[1][0] = 90
assert hdu.data._coldefs._arrays[1][0] == 90
assert hdu.data._coldefs.columns[1].array[0] == 90
assert hdu.columns._arrays[1][0] == 90
assert hdu.columns.columns[1].array[0] == 90
assert hdu.data[0][1] == 90
hdu.columns.columns[1].array[0] = 80
assert hdu.data._coldefs._arrays[1][0] == 80
assert hdu.data._coldefs.columns[1].array[0] == 80
assert hdu.columns._arrays[1][0] == 80
assert hdu.columns.columns[1].array[0] == 80
assert hdu.data[0][1] == 80
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:647:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestTableFunctions.test_merge_tables _____________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000018c19558>
def test_merge_tables(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.writeto(self.temp('table1.fits'))
counts = np.array([412, 434, 408, 417])
names = np.array(['NGC5', 'NGC6', 'NGC7', 'NCG8'])
c1 = fits.Column(name='target1', format='10A', array=names)
c2 = fits.Column(name='counts1', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes1', format='A10')
c4 = fits.Column(name='spectrum1', format='5E')
c5 = fits.Column(name='flag1', format='L', array=[0, 1, 0, 0])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.writeto(self.temp('table2.fits'))
# Merge the columns of table 2 after the columns of table 1
# The column names are assumed to be different
# Open the two files we want to append
t1 = fits.open(self.temp('table1.fits'))
t2 = fits.open(self.temp('table2.fits'))
hdu = fits.BinTableHDU.from_columns(t1[1].columns + t2[1].columns)
z = np.array([0., 0., 0., 0., 0.], dtype=np.float32)
array = np.rec.array(
[('NGC1', 312, '', z, True, 'NGC5', 412, '', z, False),
('NGC2', 334, '', z, False, 'NGC6', 434, '', z, True),
('NGC3', 308, '', z, True, 'NGC7', 408, '', z, False),
('NCG4', 317, '', z, True, 'NCG8', 417, '', z, False)],
formats='a10,u4,a10,5f4,l,a10,u4,a10,5f4,l')
assert comparerecords(hdu.data, array)
hdu.writeto(self.temp('newtable.fits'))
# Verify that all of the references to the data point to the same
# numarray
hdu.data[0][1] = 300
assert hdu.data._coldefs._arrays[1][0] == 300
assert hdu.data._coldefs.columns[1].array[0] == 300
assert hdu.columns._arrays[1][0] == 300
assert hdu.columns.columns[1].array[0] == 300
assert hdu.data[0][1] == 300
hdu.data._coldefs._arrays[1][0] = 200
assert hdu.data._coldefs._arrays[1][0] == 200
assert hdu.data._coldefs.columns[1].array[0] == 200
assert hdu.columns._arrays[1][0] == 200
assert hdu.columns.columns[1].array[0] == 200
assert hdu.data[0][1] == 200
hdu.data._coldefs.columns[1].array[0] = 100
assert hdu.data._coldefs._arrays[1][0] == 100
assert hdu.data._coldefs.columns[1].array[0] == 100
assert hdu.columns._arrays[1][0] == 100
assert hdu.columns.columns[1].array[0] == 100
assert hdu.data[0][1] == 100
hdu.columns._arrays[1][0] = 90
assert hdu.data._coldefs._arrays[1][0] == 90
assert hdu.data._coldefs.columns[1].array[0] == 90
assert hdu.columns._arrays[1][0] == 90
assert hdu.columns.columns[1].array[0] == 90
assert hdu.data[0][1] == 90
hdu.columns.columns[1].array[0] = 80
assert hdu.data._coldefs._arrays[1][0] == 80
assert hdu.data._coldefs.columns[1].array[0] == 80
assert hdu.columns._arrays[1][0] == 80
assert hdu.columns.columns[1].array[0] == 80
assert hdu.data[0][1] == 80
info = [(0, 'PRIMARY', 1, 'PrimaryHDU', 4, (), '', ''),
(1, '', 1, 'BinTableHDU', 30, '4R x 10C',
'[10A, J, 10A, 5E, L, 10A, J, 10A, 5E, L]', '')]
assert fits.info(self.temp('newtable.fits'), output=False) == info
hdul = fits.open(self.temp('newtable.fits'))
hdu = hdul[1]
assert (hdu.columns.names ==
['target', 'counts', 'notes', 'spectrum', 'flag', 'target1',
'counts1', 'notes1', 'spectrum1', 'flag1'])
z = np.array([0., 0., 0., 0., 0.], dtype=np.float32)
array = np.rec.array(
[('NGC1', 312, '', z, True, 'NGC5', 412, '', z, False),
('NGC2', 334, '', z, False, 'NGC6', 434, '', z, True),
('NGC3', 308, '', z, True, 'NGC7', 408, '', z, False),
('NCG4', 317, '', z, True, 'NCG8', 417, '', z, False)],
formats='a10,u4,a10,5f4,l,a10,u4,a10,5f4,l')
assert comparerecords(hdu.data, array)
# Same verification from the file
hdu.data[0][1] = 300
assert hdu.data._coldefs._arrays[1][0] == 300
assert hdu.data._coldefs.columns[1].array[0] == 300
assert hdu.columns._arrays[1][0] == 300
assert hdu.columns.columns[1].array[0] == 300
assert hdu.data[0][1] == 300
hdu.data._coldefs._arrays[1][0] = 200
assert hdu.data._coldefs._arrays[1][0] == 200
assert hdu.data._coldefs.columns[1].array[0] == 200
assert hdu.columns._arrays[1][0] == 200
assert hdu.columns.columns[1].array[0] == 200
assert hdu.data[0][1] == 200
hdu.data._coldefs.columns[1].array[0] = 100
assert hdu.data._coldefs._arrays[1][0] == 100
assert hdu.data._coldefs.columns[1].array[0] == 100
assert hdu.columns._arrays[1][0] == 100
assert hdu.columns.columns[1].array[0] == 100
assert hdu.data[0][1] == 100
hdu.columns._arrays[1][0] = 90
assert hdu.data._coldefs._arrays[1][0] == 90
assert hdu.data._coldefs.columns[1].array[0] == 90
assert hdu.columns._arrays[1][0] == 90
assert hdu.columns.columns[1].array[0] == 90
assert hdu.data[0][1] == 90
hdu.columns.columns[1].array[0] = 80
assert hdu.data._coldefs._arrays[1][0] == 80
assert hdu.data._coldefs.columns[1].array[0] == 80
assert hdu.columns._arrays[1][0] == 80
assert hdu.columns.columns[1].array[0] == 80
assert hdu.data[0][1] == 80
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:817:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestTableFunctions.test_mask_array ______________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000f285638>
def test_mask_array(self):
t = fits.open(self.data('table.fits'))
tbdata = t[1].data
mask = tbdata.field('V_mag') > 12
newtbdata = tbdata[mask]
hdu = fits.BinTableHDU(newtbdata)
hdu.writeto(self.temp('newtable.fits'))
hdul = fits.open(self.temp('newtable.fits'))
# match to a regex rather than a specific string.
expect = r"\[\('NGC1002',\s+12.3[0-9]*\) \(\'NGC1003\',\s+15.[0-9]+\)\]"
assert re.match(expect, str(hdu.data))
assert re.match(expect, str(hdul[1].data))
> t.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:862:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestTableFunctions.test_slice_a_row ______________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001466b2f0>
def test_slice_a_row(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.writeto(self.temp('table1.fits'))
t1 = fits.open(self.temp('table1.fits'))
row = t1[1].data[2]
assert row['counts'] == 308
a, b, c = row[1:4]
assert a == counts[2]
assert b == ''
assert (c == np.array([0., 0., 0., 0., 0.], dtype=np.float32)).all()
row['counts'] = 310
assert row['counts'] == 310
row[1] = 315
assert row['counts'] == 315
assert row[1:4]['counts'] == 315
pytest.raises(KeyError, lambda r: r[1:4]['flag'], row)
row[1:4]['counts'] = 300
assert row[1:4]['counts'] == 300
assert row['counts'] == 300
row[1:4][0] = 400
assert row[1:4]['counts'] == 400
row[1:4]['counts'] = 300
assert row[1:4]['counts'] == 300
# Test stepping for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/59
row[1:4][::-1][-1] = 500
assert row[1:4]['counts'] == 500
row[1:4:2][0] = 300
assert row[1:4]['counts'] == 300
pytest.raises(KeyError, lambda r: r[1:4]['flag'], row)
assert row[1:4].field(0) == 300
assert row[1:4].field('counts') == 300
pytest.raises(KeyError, row[1:4].field, 'flag')
row[1:4].setfield('counts', 500)
assert row[1:4].field(0) == 500
pytest.raises(KeyError, row[1:4].setfield, 'flag', False)
assert t1[1].data._coldefs._arrays[1][2] == 500
assert t1[1].data._coldefs.columns[1].array[2] == 500
assert t1[1].columns._arrays[1][2] == 500
assert t1[1].columns.columns[1].array[2] == 500
assert t1[1].data[2][1] == 500
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:927:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestTableFunctions.test_fits_record_len ____________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000187bf328>
def test_fits_record_len(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.writeto(self.temp('table1.fits'))
t1 = fits.open(self.temp('table1.fits'))
assert len(t1[1].data[0]) == 5
assert len(t1[1].data[0][0:4]) == 4
assert len(t1[1].data[0][0:5]) == 5
assert len(t1[1].data[0][0:6]) == 5
assert len(t1[1].data[0][0:7]) == 5
assert len(t1[1].data[0][1:4]) == 3
assert len(t1[1].data[0][1:5]) == 4
assert len(t1[1].data[0][1:6]) == 4
assert len(t1[1].data[0][1:7]) == 4
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:953:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_verify_data_references ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001a397f68>
def test_verify_data_references(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
# Verify that original ColDefs object has independent Column
# objects.
assert id(coldefs.columns[0]) != id(c1)
# Verify that original ColDefs object has independent ndarray
# objects.
assert id(coldefs.columns[0].array) != id(names)
# Verify that original ColDefs object references the same data
# object as the original Column object.
assert id(coldefs.columns[0].array) == id(c1.array)
assert id(coldefs.columns[0].array) == id(coldefs._arrays[0])
# Verify new HDU has an independent ColDefs object.
assert id(coldefs) != id(tbhdu.columns)
# Verify new HDU has independent Column objects.
assert id(coldefs.columns[0]) != id(tbhdu.columns.columns[0])
# Verify new HDU has independent ndarray objects.
assert (id(coldefs.columns[0].array) !=
id(tbhdu.columns.columns[0].array))
# Verify that both ColDefs objects in the HDU reference the same
# Coldefs object.
assert id(tbhdu.columns) == id(tbhdu.data._coldefs)
# Verify that all ndarray objects within the HDU reference the
# same ndarray.
assert (id(tbhdu.data._coldefs.columns[0].array) ==
id(tbhdu.data._coldefs._arrays[0]))
assert (id(tbhdu.data._coldefs.columns[0].array) ==
id(tbhdu.columns.columns[0].array))
assert (id(tbhdu.data._coldefs.columns[0].array) ==
id(tbhdu.columns._arrays[0]))
tbhdu.writeto(self.temp('table1.fits'))
t1 = fits.open(self.temp('table1.fits'))
t1[1].data[0][1] = 213
assert t1[1].data[0][1] == 213
assert t1[1].data._coldefs._arrays[1][0] == 213
assert t1[1].data._coldefs.columns[1].array[0] == 213
assert t1[1].columns._arrays[1][0] == 213
assert t1[1].columns.columns[1].array[0] == 213
t1[1].data._coldefs._arrays[1][0] = 100
assert t1[1].data[0][1] == 100
assert t1[1].data._coldefs._arrays[1][0] == 100
assert t1[1].data._coldefs.columns[1].array[0] == 100
assert t1[1].columns._arrays[1][0] == 100
assert t1[1].columns.columns[1].array[0] == 100
t1[1].data._coldefs.columns[1].array[0] = 500
assert t1[1].data[0][1] == 500
assert t1[1].data._coldefs._arrays[1][0] == 500
assert t1[1].data._coldefs.columns[1].array[0] == 500
assert t1[1].columns._arrays[1][0] == 500
assert t1[1].columns.columns[1].array[0] == 500
t1[1].columns._arrays[1][0] = 600
assert t1[1].data[0][1] == 600
assert t1[1].data._coldefs._arrays[1][0] == 600
assert t1[1].data._coldefs.columns[1].array[0] == 600
assert t1[1].columns._arrays[1][0] == 600
assert t1[1].columns.columns[1].array[0] == 600
t1[1].columns.columns[1].array[0] = 800
assert t1[1].data[0][1] == 800
assert t1[1].data._coldefs._arrays[1][0] == 800
assert t1[1].data._coldefs.columns[1].array[0] == 800
assert t1[1].columns._arrays[1][0] == 800
assert t1[1].columns.columns[1].array[0] == 800
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1178:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_new_table_with_ndarray ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000f156cd0>
def test_new_table_with_ndarray(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu1 = fits.BinTableHDU.from_columns(tbhdu.data.view(np.ndarray))
# Verify that all ndarray objects within the HDU reference the
# same ndarray.
assert (id(tbhdu1.data._coldefs.columns[0].array) ==
id(tbhdu1.data._coldefs._arrays[0]))
assert (id(tbhdu1.data._coldefs.columns[0].array) ==
id(tbhdu1.columns.columns[0].array))
assert (id(tbhdu1.data._coldefs.columns[0].array) ==
id(tbhdu1.columns._arrays[0]))
# Ensure I can change the value of one data element and it effects
# all of the others.
tbhdu1.data[0][1] = 213
assert tbhdu1.data[0][1] == 213
assert tbhdu1.data._coldefs._arrays[1][0] == 213
assert tbhdu1.data._coldefs.columns[1].array[0] == 213
assert tbhdu1.columns._arrays[1][0] == 213
assert tbhdu1.columns.columns[1].array[0] == 213
tbhdu1.data._coldefs._arrays[1][0] = 100
assert tbhdu1.data[0][1] == 100
assert tbhdu1.data._coldefs._arrays[1][0] == 100
assert tbhdu1.data._coldefs.columns[1].array[0] == 100
assert tbhdu1.columns._arrays[1][0] == 100
assert tbhdu1.columns.columns[1].array[0] == 100
tbhdu1.data._coldefs.columns[1].array[0] = 500
assert tbhdu1.data[0][1] == 500
assert tbhdu1.data._coldefs._arrays[1][0] == 500
assert tbhdu1.data._coldefs.columns[1].array[0] == 500
assert tbhdu1.columns._arrays[1][0] == 500
assert tbhdu1.columns.columns[1].array[0] == 500
tbhdu1.columns._arrays[1][0] = 600
assert tbhdu1.data[0][1] == 600
assert tbhdu1.data._coldefs._arrays[1][0] == 600
assert tbhdu1.data._coldefs.columns[1].array[0] == 600
assert tbhdu1.columns._arrays[1][0] == 600
assert tbhdu1.columns.columns[1].array[0] == 600
tbhdu1.columns.columns[1].array[0] = 800
assert tbhdu1.data[0][1] == 800
assert tbhdu1.data._coldefs._arrays[1][0] == 800
assert tbhdu1.data._coldefs.columns[1].array[0] == 800
assert tbhdu1.columns._arrays[1][0] == 800
assert tbhdu1.columns.columns[1].array[0] == 800
tbhdu1.writeto(self.temp('table1.fits'))
t1 = fits.open(self.temp('table1.fits'))
t1[1].data[0][1] = 213
assert t1[1].data[0][1] == 213
assert t1[1].data._coldefs._arrays[1][0] == 213
assert t1[1].data._coldefs.columns[1].array[0] == 213
assert t1[1].columns._arrays[1][0] == 213
assert t1[1].columns.columns[1].array[0] == 213
t1[1].data._coldefs._arrays[1][0] = 100
assert t1[1].data[0][1] == 100
assert t1[1].data._coldefs._arrays[1][0] == 100
assert t1[1].data._coldefs.columns[1].array[0] == 100
assert t1[1].columns._arrays[1][0] == 100
assert t1[1].columns.columns[1].array[0] == 100
t1[1].data._coldefs.columns[1].array[0] = 500
assert t1[1].data[0][1] == 500
assert t1[1].data._coldefs._arrays[1][0] == 500
assert t1[1].data._coldefs.columns[1].array[0] == 500
assert t1[1].columns._arrays[1][0] == 500
assert t1[1].columns.columns[1].array[0] == 500
t1[1].columns._arrays[1][0] = 600
assert t1[1].data[0][1] == 600
assert t1[1].data._coldefs._arrays[1][0] == 600
assert t1[1].data._coldefs.columns[1].array[0] == 600
assert t1[1].columns._arrays[1][0] == 600
assert t1[1].columns.columns[1].array[0] == 600
t1[1].columns.columns[1].array[0] = 800
assert t1[1].data[0][1] == 800
assert t1[1].data._coldefs._arrays[1][0] == 800
assert t1[1].data._coldefs.columns[1].array[0] == 800
assert t1[1].columns._arrays[1][0] == 800
assert t1[1].columns.columns[1].array[0] == 800
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1283:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestTableFunctions.test_new_table_with_fits_rec ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000cb2b558>
def test_new_table_with_fits_rec(self):
counts = np.array([312, 334, 308, 317])
names = np.array(['NGC1', 'NGC2', 'NGC3', 'NCG4'])
c1 = fits.Column(name='target', format='10A', array=names)
c2 = fits.Column(name='counts', format='J', unit='DN', array=counts)
c3 = fits.Column(name='notes', format='A10')
c4 = fits.Column(name='spectrum', format='5E')
c5 = fits.Column(name='flag', format='L', array=[1, 0, 1, 1])
coldefs = fits.ColDefs([c1, c2, c3, c4, c5])
tbhdu = fits.BinTableHDU.from_columns(coldefs)
tbhdu.data[0][1] = 213
assert tbhdu.data[0][1] == 213
assert tbhdu.data._coldefs._arrays[1][0] == 213
assert tbhdu.data._coldefs.columns[1].array[0] == 213
assert tbhdu.columns._arrays[1][0] == 213
assert tbhdu.columns.columns[1].array[0] == 213
tbhdu.data._coldefs._arrays[1][0] = 100
assert tbhdu.data[0][1] == 100
assert tbhdu.data._coldefs._arrays[1][0] == 100
assert tbhdu.data._coldefs.columns[1].array[0] == 100
assert tbhdu.columns._arrays[1][0] == 100
assert tbhdu.columns.columns[1].array[0] == 100
tbhdu.data._coldefs.columns[1].array[0] = 500
assert tbhdu.data[0][1] == 500
assert tbhdu.data._coldefs._arrays[1][0] == 500
assert tbhdu.data._coldefs.columns[1].array[0] == 500
assert tbhdu.columns._arrays[1][0] == 500
assert tbhdu.columns.columns[1].array[0] == 500
tbhdu.columns._arrays[1][0] = 600
assert tbhdu.data[0][1] == 600
assert tbhdu.data._coldefs._arrays[1][0] == 600
assert tbhdu.data._coldefs.columns[1].array[0] == 600
assert tbhdu.columns._arrays[1][0] == 600
assert tbhdu.columns.columns[1].array[0] == 600
tbhdu.columns.columns[1].array[0] = 800
assert tbhdu.data[0][1] == 800
assert tbhdu.data._coldefs._arrays[1][0] == 800
assert tbhdu.data._coldefs.columns[1].array[0] == 800
assert tbhdu.columns._arrays[1][0] == 800
assert tbhdu.columns.columns[1].array[0] == 800
tbhdu.columns.columns[1].array[0] = 312
tbhdu.writeto(self.temp('table1.fits'))
t1 = fits.open(self.temp('table1.fits'))
t1[1].data[0][1] = 1
fr = t1[1].data
assert t1[1].data[0][1] == 1
assert t1[1].data._coldefs._arrays[1][0] == 1
assert t1[1].data._coldefs.columns[1].array[0] == 1
assert t1[1].columns._arrays[1][0] == 1
assert t1[1].columns.columns[1].array[0] == 1
assert fr[0][1] == 1
assert fr._coldefs._arrays[1][0] == 1
assert fr._coldefs.columns[1].array[0] == 1
fr._coldefs.columns[1].array[0] = 312
tbhdu1 = fits.BinTableHDU.from_columns(fr)
i = 0
for row in tbhdu1.data:
for j in range(len(row)):
if isinstance(row[j], np.ndarray):
assert (row[j] == tbhdu.data[i][j]).all()
else:
assert row[j] == tbhdu.data[i][j]
i = i + 1
tbhdu1.data[0][1] = 213
assert t1[1].data[0][1] == 312
assert t1[1].data._coldefs._arrays[1][0] == 312
assert t1[1].data._coldefs.columns[1].array[0] == 312
assert t1[1].columns._arrays[1][0] == 312
assert t1[1].columns.columns[1].array[0] == 312
assert fr[0][1] == 312
assert fr._coldefs._arrays[1][0] == 312
assert fr._coldefs.columns[1].array[0] == 312
assert tbhdu1.data[0][1] == 213
assert tbhdu1.data._coldefs._arrays[1][0] == 213
assert tbhdu1.data._coldefs.columns[1].array[0] == 213
assert tbhdu1.columns._arrays[1][0] == 213
assert tbhdu1.columns.columns[1].array[0] == 213
t1[1].data[0][1] = 10
assert t1[1].data[0][1] == 10
assert t1[1].data._coldefs._arrays[1][0] == 10
assert t1[1].data._coldefs.columns[1].array[0] == 10
assert t1[1].columns._arrays[1][0] == 10
assert t1[1].columns.columns[1].array[0] == 10
assert fr[0][1] == 10
assert fr._coldefs._arrays[1][0] == 10
assert fr._coldefs.columns[1].array[0] == 10
assert tbhdu1.data[0][1] == 213
assert tbhdu1.data._coldefs._arrays[1][0] == 213
assert tbhdu1.data._coldefs.columns[1].array[0] == 213
assert tbhdu1.columns._arrays[1][0] == 213
assert tbhdu1.columns.columns[1].array[0] == 213
tbhdu1.data._coldefs._arrays[1][0] = 666
assert t1[1].data[0][1] == 10
assert t1[1].data._coldefs._arrays[1][0] == 10
assert t1[1].data._coldefs.columns[1].array[0] == 10
assert t1[1].columns._arrays[1][0] == 10
assert t1[1].columns.columns[1].array[0] == 10
assert fr[0][1] == 10
assert fr._coldefs._arrays[1][0] == 10
assert fr._coldefs.columns[1].array[0] == 10
assert tbhdu1.data[0][1] == 666
assert tbhdu1.data._coldefs._arrays[1][0] == 666
assert tbhdu1.data._coldefs.columns[1].array[0] == 666
assert tbhdu1.columns._arrays[1][0] == 666
assert tbhdu1.columns.columns[1].array[0] == 666
> t1.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1412:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_fits_rec_column_access ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000016b188e0>
def test_fits_rec_column_access(self):
t = fits.open(self.data('table.fits'))
tbdata = t[1].data
assert (tbdata.V_mag == tbdata.field('V_mag')).all()
assert (tbdata.V_mag == tbdata['V_mag']).all()
> t.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1592:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestTableFunctions.test_table_with_zero_width_column _____________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000129c23a0>
def test_table_with_zero_width_column(self):
hdul = fits.open(self.data('zerowidth.fits'))
tbhdu = hdul[2] # This HDU contains a zero-width column 'ORBPARM'
assert 'ORBPARM' in tbhdu.columns.names
# The ORBPARM column should not be in the data, though the data should
# be readable
assert 'ORBPARM' in tbhdu.data.names
assert 'ORBPARM' in tbhdu.data.dtype.names
# Verify that some of the data columns are still correctly accessible
# by name
assert tbhdu.data[0]['ANNAME'] == 'VLA:_W16'
assert comparefloats(
tbhdu.data[0]['STABXYZ'],
np.array([499.85566663, -1317.99231554, -735.18866164],
dtype=np.float64))
assert tbhdu.data[0]['NOSTA'] == 1
assert tbhdu.data[0]['MNTSTA'] == 0
assert tbhdu.data[-1]['ANNAME'] == 'VPT:_OUT'
assert comparefloats(
tbhdu.data[-1]['STABXYZ'],
np.array([0.0, 0.0, 0.0], dtype=np.float64))
assert tbhdu.data[-1]['NOSTA'] == 29
assert tbhdu.data[-1]['MNTSTA'] == 0
hdul.writeto(self.temp('newtable.fits'))
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1618:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_string_column_padding _________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000022026838>
def test_string_column_padding(self):
a = ['img1', 'img2', 'img3a', 'p']
s = 'img1\x00\x00\x00\x00\x00\x00' \
'img2\x00\x00\x00\x00\x00\x00' \
'img3a\x00\x00\x00\x00\x00' \
'p\x00\x00\x00\x00\x00\x00\x00\x00\x00'
acol = fits.Column(name='MEMNAME', format='A10',
array=chararray.array(a))
ahdu = fits.BinTableHDU.from_columns([acol])
assert ahdu.data.tostring().decode('raw-unicode-escape') == s
ahdu.writeto(self.temp('newtable.fits'))
with fits.open(self.temp('newtable.fits')) as hdul:
assert hdul[1].data.tostring().decode('raw-unicode-escape') == s
> assert (hdul[1].data['MEMNAME'] == a).all()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1655:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestTableFunctions.test_multi_dimensional_columns _______________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000010e9b910>
def test_multi_dimensional_columns(self):
"""
Tests the multidimensional column implementation with both numeric
arrays and string arrays.
"""
data = np.rec.array(
[([0, 1, 2, 3, 4, 5], 'row1' * 2),
([6, 7, 8, 9, 0, 1], 'row2' * 2),
([2, 3, 4, 5, 6, 7], 'row3' * 2)], formats='6i4,a8')
thdu = fits.BinTableHDU.from_columns(data)
# Modify the TDIM fields to my own specification
thdu.header['TDIM1'] = '(2,3)'
thdu.header['TDIM2'] = '(4,2)'
thdu.writeto(self.temp('newtable.fits'))
with fits.open(self.temp('newtable.fits')) as hdul:
thdu = hdul[1]
c1 = thdu.data.field(0)
c2 = thdu.data.field(1)
assert c1.shape == (3, 3, 2)
assert c2.shape == (3, 2)
assert (c1 == np.array([[[0, 1], [2, 3], [4, 5]],
[[6, 7], [8, 9], [0, 1]],
[[2, 3], [4, 5], [6, 7]]])).all()
> assert (c2 == np.array([['row1', 'row1'],
['row2', 'row2'],
['row3', 'row3']])).all()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1705:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______ TestTableFunctions.test_bin_table_init_from_string_array_column ________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000022caa5d0>
def test_bin_table_init_from_string_array_column(self):
"""
Tests two ways of creating a new `BinTableHDU` from a column of
string arrays.
This tests for a couple different regressions, and ensures that
both BinTableHDU(data=arr) and BinTableHDU.from_columns(arr) work
equivalently.
Some of this is redundant with the following test, but checks some
subtly different cases.
"""
data = [[b'abcd', b'efgh'],
[b'ijkl', b'mnop'],
[b'qrst', b'uvwx']]
arr = np.array([(data,), (data,), (data,), (data,), (data,)],
dtype=[('S', '(3, 2)S4')])
with catch_warnings() as w:
tbhdu1 = fits.BinTableHDU(data=arr)
assert len(w) == 0
def test_dims_and_roundtrip(tbhdu):
assert tbhdu.data['S'].shape == (5, 3, 2)
assert tbhdu.data['S'].dtype.str.endswith('U4')
tbhdu.writeto(self.temp('test.fits'), overwrite=True)
with fits.open(self.temp('test.fits')) as hdul:
tbhdu2 = hdul[1]
assert tbhdu2.header['TDIM1'] == '(4,2,3)'
assert tbhdu2.data['S'].shape == (5, 3, 2)
assert tbhdu.data['S'].dtype.str.endswith('U4')
assert np.all(tbhdu2.data['S'] == tbhdu.data['S'])
> test_dims_and_roundtrip(tbhdu1)
pypy/site-packages/astropy/io/fits/tests/test_table.py:1779:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:1777: in test_dims_and_roundtrip
assert np.all(tbhdu2.data['S'] == tbhdu.data['S'])
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestTableFunctions.test_columns_with_truncating_tdim _____________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001b68b3d0>
def test_columns_with_truncating_tdim(self):
"""
According to the FITS standard (section 7.3.2):
If the number of elements in the array implied by the TDIMn is less
than the allocated size of the ar- ray in the FITS file, then the
unused trailing elements should be interpreted as containing
undefined fill values.
*deep sigh* What this means is if a column has a repeat count larger
than the number of elements indicated by its TDIM (ex: TDIM1 = '(2,2)',
but TFORM1 = 6I), then instead of this being an outright error we are
to take the first 4 elements as implied by the TDIM and ignore the
additional two trailing elements.
"""
# It's hard to even successfully create a table like this. I think
# it *should* be difficult, but once created it should at least be
# possible to read.
arr1 = [[b'ab', b'cd'], [b'ef', b'gh'], [b'ij', b'kl']]
arr2 = [1, 2, 3, 4, 5]
arr = np.array([(arr1, arr2), (arr1, arr2)],
dtype=[('a', '(3, 2)S2'), ('b', '5i8')])
tbhdu = fits.BinTableHDU(data=arr)
tbhdu.writeto(self.temp('test.fits'))
with open(self.temp('test.fits'), 'rb') as f:
raw_bytes = f.read()
# Artificially truncate TDIM in the header; this seems to be the
# easiest way to do this while getting around Astropy's insistence on the
# data and header matching perfectly; again, we have no interest in
# making it possible to write files in this format, only read them
with open(self.temp('test.fits'), 'wb') as f:
f.write(raw_bytes.replace(b'(2,2,3)', b'(2,2,2)'))
with fits.open(self.temp('test.fits')) as hdul:
tbhdu2 = hdul[1]
assert tbhdu2.header['TDIM1'] == '(2,2,2)'
assert tbhdu2.header['TFORM1'] == '12A'
for row in tbhdu2.data:
assert np.all(row['a'] == [['ab', 'cd'], ['ef', 'gh']])
> assert np.all(row['b'] == [1, 2, 3, 4, 5])
pypy/site-packages/astropy/io/fits/tests/test_table.py:1828:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestTableFunctions.test_string_array_round_trip ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000022400f38>
def test_string_array_round_trip(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/201"""
data = [['abc', 'def', 'ghi'],
['jkl', 'mno', 'pqr'],
['stu', 'vwx', 'yz ']]
recarr = np.rec.array([(data,), (data,)], formats=['(3,3)S3'])
t = fits.BinTableHDU(data=recarr)
t.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as h:
assert 'TDIM1' in h[1].header
assert h[1].header['TDIM1'] == '(3,3,3)'
assert len(h[1].data) == 2
assert len(h[1].data[0]) == 1
> assert (h[1].data.field(0)[0] ==
np.char.decode(recarr.field(0)[0], 'ascii')).all()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1847:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ TestTableFunctions.test_new_table_with_nd_column _______________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000e107a60>
def test_new_table_with_nd_column(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/3
"""
arra = np.array(['a', 'b'], dtype='|S1')
arrb = np.array([['a', 'bc'], ['cd', 'e']], dtype='|S2')
arrc = np.array([[[1, 2], [3, 4]], [[5, 6], [7, 8]]])
cols = [
fits.Column(name='str', format='1A', array=arra),
fits.Column(name='strarray', format='4A', dim='(2,2)',
array=arrb),
fits.Column(name='intarray', format='4I', dim='(2, 2)',
array=arrc)
]
hdu = fits.BinTableHDU.from_columns(fits.ColDefs(cols))
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as h:
# Need to force string arrays to byte arrays in order to compare
# correctly on Python 3
assert (h[1].data['str'].encode('ascii') == arra).all()
assert (h[1].data['strarray'].encode('ascii') == arrb).all()
> assert (h[1].data['intarray'] == arrc).all()
pypy/site-packages/astropy/io/fits/tests/test_table.py:1889:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestTableFunctions.test_mismatched_tform_and_tdim _______________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000cd155c8>
def test_mismatched_tform_and_tdim(self):
"""Normally the product of the dimensions listed in a TDIMn keyword
must be less than or equal to the repeat count in the TFORMn keyword.
This tests that this works if less than (treating the trailing bytes
as unspecified fill values per the FITS standard) and fails if the
dimensions specified by TDIMn are greater than the repeat count.
"""
arra = np.array([[[1, 2], [3, 4]], [[5, 6], [7, 8]]])
arrb = np.array([[[9, 10], [11, 12]], [[13, 14], [15, 16]]])
cols = [fits.Column(name='a', format='20I', dim='(2,2)',
array=arra),
fits.Column(name='b', format='4I', dim='(2,2)',
array=arrb)]
# The first column has the mismatched repeat count
hdu = fits.BinTableHDU.from_columns(fits.ColDefs(cols))
hdu.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as h:
assert h[1].header['TFORM1'] == '20I'
assert h[1].header['TFORM2'] == '4I'
assert h[1].header['TDIM1'] == h[1].header['TDIM2'] == '(2,2)'
assert (h[1].data['a'] == arra).all()
assert (h[1].data['b'] == arrb).all()
> assert h[1].data.itemsize == 48 # 16-bits times 24
pypy/site-packages/astropy/io/fits/tests/test_table.py:1918:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestTableFunctions.test_tdim_of_size_one ___________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000016b18988>
def test_tdim_of_size_one(self):
"""Regression test for https://github.com/astropy/astropy/pull/3580"""
with fits.open(self.data('tdim.fits')) as hdulist:
> assert hdulist[1].data['V_mag'].shape == (3, 1, 1)
pypy/site-packages/astropy/io/fits/tests/test_table.py:1929:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________ TestTableFunctions.test_slicing ________________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000133d0100>
def test_slicing(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/52"""
with fits.open(self.data('table.fits')) as f:
> data = f[1].data
pypy/site-packages/astropy/io/fits/tests/test_table.py:1935:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestTableFunctions.test_array_slicing _____________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000220682c0>
def test_array_slicing(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/55"""
with fits.open(self.data('table.fits')) as f:
> data = f[1].data
pypy/site-packages/astropy/io/fits/tests/test_table.py:1953:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestTableFunctions.test_array_broadcasting __________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001849a218>
def test_array_broadcasting(self):
"""
Regression test for https://github.com/spacetelescope/PyFITS/pull/48
"""
with fits.open(self.data('table.fits')) as hdu:
data = hdu[1].data
data['V_mag'] = 0
assert np.all(data['V_mag'] == 0)
data['V_mag'] = 1
assert np.all(data['V_mag'] == 1)
for container in (list, tuple, np.array):
data['V_mag'] = container([1, 2, 3])
> assert np.array_equal(data['V_mag'], np.array([1, 2, 3]))
pypy/site-packages/astropy/io/fits/tests/test_table.py:1980:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_array_slicing_readonly ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000002239b520>
def test_array_slicing_readonly(self):
"""
Like test_array_slicing but with the file opened in 'readonly' mode.
Regression test for a crash when slicing readonly memmap'd tables.
"""
with fits.open(self.data('table.fits'), mode='readonly') as f:
> data = f[1].data
pypy/site-packages/astropy/io/fits/tests/test_table.py:1989:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestTableFunctions.test_dump_load_round_trip _________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000021646a68>
def test_dump_load_round_trip(self):
"""
A simple test of the dump/load methods; dump the data, column, and
header files and try to reload the table from them.
"""
hdul = fits.open(self.data('table.fits'))
tbhdu = hdul[1]
datafile = self.temp('data.txt')
cdfile = self.temp('coldefs.txt')
hfile = self.temp('header.txt')
tbhdu.dump(datafile, cdfile, hfile)
new_tbhdu = fits.BinTableHDU.load(datafile, cdfile, hfile)
assert comparerecords(tbhdu.data, new_tbhdu.data)
# Double check that the headers are equivalent
assert str(tbhdu.header) == str(new_tbhdu.header)
> hdul.close()
pypy/site-packages/astropy/io/fits/tests/test_table.py:2021:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_table_from_bool_fields ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000016d3cf00>
def test_table_from_bool_fields(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/113
Tests creating a table from a recarray containing numpy.bool columns.
"""
array = np.rec.array([(True, False), (False, True)], formats='|b1,|b1')
thdu = fits.BinTableHDU.from_columns(array)
assert thdu.columns.formats == ['L', 'L']
assert comparerecords(thdu.data, array)
# Test round trip
thdu.writeto(self.temp('table.fits'))
> data = fits.getdata(self.temp('table.fits'), ext=1)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2125:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestTableFunctions.test_bool_column_update __________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000f149ad0>
def test_bool_column_update(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/139"""
c1 = fits.Column('F1', 'L', array=[True, False])
c2 = fits.Column('F2', 'L', array=[False, True])
thdu = fits.BinTableHDU.from_columns(fits.ColDefs([c1, c2]))
thdu.writeto(self.temp('table.fits'))
with fits.open(self.temp('table.fits'), mode='update') as hdul:
hdul[1].data['F1'][1] = True
> hdul[1].data['F2'][0] = True
pypy/site-packages/astropy/io/fits/tests/test_table.py:2151:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestTableFunctions.test_missing_tnull _____________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000c8b4b80>
def test_missing_tnull(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/197"""
c = fits.Column('F1', 'A3', null='---',
array=np.array(['1.0', '2.0', '---', '3.0']),
ascii=True)
table = fits.TableHDU.from_columns([c])
table.writeto(self.temp('test.fits'))
# Now let's delete the TNULL1 keyword, making this essentially
# unreadable
with fits.open(self.temp('test.fits'), mode='update') as h:
h[1].header['TFORM1'] = 'E3'
del h[1].header['TNULL1']
with fits.open(self.temp('test.fits')) as h:
> pytest.raises(ValueError, lambda: h[1].data['F1'])
pypy/site-packages/astropy/io/fits/tests/test_table.py:2173:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestTableFunctions.test_blank_field_zero ___________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000012a7d910>
def test_blank_field_zero(self):
"""Regression test for https://github.com/astropy/astropy/issues/5134
Blank values in numerical columns of ASCII tables should be replaced
with zeros, so they can be loaded into numpy arrays.
When a TNULL value is set and there are blank fields not equal to that
value, they should be replaced with zeros.
"""
# Test an integer column with blank string as null
nullval1 = ' '
c1 = fits.Column('F1', format='I8', null=nullval1,
array=np.array([0, 1, 2, 3, 4]),
ascii=True)
table = fits.TableHDU.from_columns([c1])
table.writeto(self.temp('ascii_null.fits'))
# Replace the 1st col, 3rd row, with a null field.
with open(self.temp('ascii_null.fits'), mode='r+') as h:
nulled = h.read().replace('2 ', ' ')
h.seek(0)
h.write(nulled)
with fits.open(self.temp('ascii_null.fits'), memmap=True) as f:
> assert f[1].data[2][0] == 0
pypy/site-packages/astropy/io/fits/tests/test_table.py:2209:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestTableFunctions.test_table_none ______________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000161ee800>
def test_table_none(self):
"""Regression test
for https://github.com/spacetelescope/PyFITS/issues/27
"""
with fits.open(self.data('tb.fits')) as h:
h[1].data
h[1].data = None
assert isinstance(h[1].data, fits.FITS_rec)
assert len(h[1].data) == 0
> h[1].writeto(self.temp('test.fits'))
pypy/site-packages/astropy/io/fits/tests/test_table.py:2247:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_unncessary_table_load _________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000124a2b48>
def test_unncessary_table_load(self):
"""Test unnecessary parsing and processing of FITS tables when writing
direclty from one FITS file to a new file without first reading the
data for user manipulation.
In other words, it should be possible to do a direct copy of the raw
data without unecessary processing of the data.
"""
with fits.open(self.data('table.fits')) as h:
> h[1].writeto(self.temp('test.fits'))
pypy/site-packages/astropy/io/fits/tests/test_table.py:2266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ TestTableFunctions.test_table_from_columns_of_other_table ___________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000019c87788>
def test_table_from_columns_of_other_table(self):
"""Tests a rare corner case where the columns of an existing table
are used to create a new table with the new_table function. In this
specific case, however, the existing table's data has not been read
yet, so new_table has to get at it through the Delayed proxy.
Note: Although this previously tested new_table it now uses
BinTableHDU.from_columns directly, around which new_table is a mere
wrapper.
"""
hdul = fits.open(self.data('table.fits'))
# Make sure the column array is in fact delayed...
assert isinstance(hdul[1].columns._arrays[0], Delayed)
# Create a new table...
t = fits.BinTableHDU.from_columns(hdul[1].columns)
# The original columns should no longer be delayed...
assert not isinstance(hdul[1].columns._arrays[0], Delayed)
t.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdul2:
> assert comparerecords(hdul[1].data, hdul2[1].data)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2302:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_bintable_to_asciitable ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000021e86448>
def test_bintable_to_asciitable(self):
"""Tests initializing a TableHDU with the data from a BinTableHDU."""
with fits.open(self.data('tb.fits')) as hdul:
tbdata = hdul[1].data
tbhdu = fits.TableHDU(data=tbdata)
with ignore_warnings():
tbhdu.writeto(self.temp('test.fits'), overwrite=True)
with fits.open(self.temp('test.fits')) as hdul2:
tbdata2 = hdul2[1].data
assert np.all(tbdata['c1'] == tbdata2['c1'])
assert np.all(tbdata['c2'] == tbdata2['c2'])
# c3 gets converted from float32 to float64 when writing
# test.fits, so cast to float32 before testing that the correct
# value is retrieved
assert np.all(tbdata['c3'].astype(np.float32) ==
tbdata2['c3'].astype(np.float32))
# c4 is a boolean column in the original table; we want ASCII
# columns to convert these to columns of 'T'/'F' strings
> assert np.all(np.where(tbdata['c4'], 'T', 'F') ==
tbdata2['c4'])
pypy/site-packages/astropy/io/fits/tests/test_table.py:2325:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000021ed3fa0>, <astropy.io.fits.hdu.table.TableHDU object at 0x0000000021ed3440>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000021ed3fa0>, <astropy.io.fits.hdu.table.TableHDU object at 0x0000000021ed3440>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000021e86448>
def test_bintable_to_asciitable(self):
"""Tests initializing a TableHDU with the data from a BinTableHDU."""
with fits.open(self.data('tb.fits')) as hdul:
tbdata = hdul[1].data
tbhdu = fits.TableHDU(data=tbdata)
with ignore_warnings():
tbhdu.writeto(self.temp('test.fits'), overwrite=True)
with fits.open(self.temp('test.fits')) as hdul2:
tbdata2 = hdul2[1].data
assert np.all(tbdata['c1'] == tbdata2['c1'])
assert np.all(tbdata['c2'] == tbdata2['c2'])
# c3 gets converted from float32 to float64 when writing
# test.fits, so cast to float32 before testing that the correct
# value is retrieved
assert np.all(tbdata['c3'].astype(np.float32) ==
tbdata2['c3'].astype(np.float32))
# c4 is a boolean column in the original table; we want ASCII
# columns to convert these to columns of 'T'/'F' strings
> assert np.all(np.where(tbdata['c4'], 'T', 'F') ==
tbdata2['c4'])
pypy/site-packages/astropy/io/fits/tests/test_table.py:2325:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestTableFunctions.test_pickle ________________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001b877280>
def test_pickle(self):
"""
Regression test for https://github.com/astropy/astropy/issues/1597
Tests for pickling FITS_rec objects
"""
# open existing FITS tables (images pickle by default, no test needed):
with fits.open(self.data('tb.fits')) as btb:
# Test column array is delayed and can pickle
assert isinstance(btb[1].columns._arrays[0], Delayed)
btb_pd = pickle.dumps(btb[1].data)
btb_pl = pickle.loads(btb_pd)
# It should not be delayed any more
assert not isinstance(btb[1].columns._arrays[0], Delayed)
> assert comparerecords(btb_pl, btb[1].data)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2346:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestTableFunctions.test_dim_column_byte_order_mismatch ____________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000001812ebb8>
def test_dim_column_byte_order_mismatch(self):
"""
When creating a table column with non-trivial TDIMn, and
big-endian array data read from an existing FITS file, the data
should not be unnecessarily byteswapped.
Regression test for https://github.com/astropy/astropy/issues/3561
"""
> data = fits.getdata(self.data('random_groups.fits'))['DATA']
pypy/site-packages/astropy/io/fits/tests/test_table.py:2387:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ TestTableFunctions.test_fits_rec_from_existing ________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000150e27c8>
def test_fits_rec_from_existing(self):
"""
Tests creating a `FITS_rec` object with `FITS_rec.from_columns`
from an existing `FITS_rec` object read from a FITS file.
This ensures that the per-column arrays are updated properly.
Regression test for https://github.com/spacetelescope/PyFITS/issues/99
"""
# The use case that revealed this problem was trying to create a new
# table from an existing table, but with additional rows so that we can
# append data from a second table (with the same column structure)
> data1 = fits.getdata(self.data('tb.fits'))
pypy/site-packages/astropy/io/fits/tests/test_table.py:2410:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestTableFunctions.test_update_string_column_inplace _____________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000c779050>
def test_update_string_column_inplace(self):
"""
Regression test for https://github.com/astropy/astropy/issues/4452
Ensure that changes to values in a string column are saved when
a file is opened in ``mode='update'``.
"""
data = np.array([('abc',)], dtype=[('a', 'S3')])
fits.writeto(self.temp('test.fits'), data)
with fits.open(self.temp('test.fits'), mode='update') as hdul:
hdul[1].data['a'][0] = 'XYZ'
> assert hdul[1].data['a'][0] == 'XYZ'
pypy/site-packages/astropy/io/fits/tests/test_table.py:2441:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ TestTableFunctions.test_dump_clobber_vs_overwrite _______________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x000000000f4744b8>
def test_dump_clobber_vs_overwrite(self):
with fits.open(self.data('table.fits')) as hdul:
tbhdu = hdul[1]
datafile = self.temp('data.txt')
cdfile = self.temp('coldefs.txt')
hfile = self.temp('header.txt')
tbhdu.dump(datafile, cdfile, hfile)
tbhdu.dump(datafile, cdfile, hfile, overwrite=True)
with catch_warnings(AstropyDeprecationWarning) as warning_lines:
tbhdu.dump(datafile, cdfile, hfile, clobber=True)
assert warning_lines[0].category == AstropyDeprecationWarning
> assert (str(warning_lines[0].message) == '"clobber" was '
'deprecated in version 2.0 and will be removed in a '
'future version. Use argument "overwrite" instead.')
pypy/site-packages/astropy/io/fits/tests/test_table.py:2541:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestTableFunctions.test_pseudo_unsigned_ints _________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x0000000016122b80>
def test_pseudo_unsigned_ints(self):
"""
Tests updating a table column containing pseudo-unsigned ints.
"""
data = np.array([1, 2, 3], dtype=np.uint32)
col = fits.Column(name='A', format='1J', bzero=2**31, array=data)
thdu = fits.BinTableHDU.from_columns([col])
thdu.writeto(self.temp('test.fits'))
# Test that the file wrote out correctly
with fits.open(self.temp('test.fits'), uint=True) as hdul:
hdu = hdul[1]
assert 'TZERO1' in hdu.header
assert hdu.header['TZERO1'] == 2**31
assert hdu.data['A'].dtype == np.dtype('uint32')
assert np.all(hdu.data['A'] == data)
# Test updating the unsigned int data
hdu.data['A'][0] = 99
> hdu.writeto(self.temp('test2.fits'))
pypy/site-packages/astropy/io/fits/tests/test_table.py:2565:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ TestTableFunctions.test_column_with_scaling __________________
self = <astropy.io.fits.tests.test_table.TestTableFunctions object at 0x00000000117b43d8>
def test_column_with_scaling(self):
"""Check that a scaled column if correctly saved once it is modified.
Regression test for https://github.com/astropy/astropy/issues/6887
"""
c1 = fits.Column(name='c1', array=np.array([1], dtype='>i2'),
format='1I', bscale=1, bzero=32768)
S = fits.HDUList([fits.PrimaryHDU(),
fits.BinTableHDU.from_columns([c1])])
# Change value in memory
S[1].data['c1'][0] = 2
S.writeto(self.temp("a.fits"))
assert S[1].data['c1'] == 2
# Read and change value in memory
with fits.open(self.temp("a.fits")) as X:
X[1].data['c1'][0] = 10
assert X[1].data['c1'][0] == 10
# Write back to file
> X.writeto(self.temp("b.fits"))
pypy/site-packages/astropy/io/fits/tests/test_table.py:2594:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ TestVLATables.test_variable_length_columns __________________
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x0000000012156e20>
def test_variable_length_columns(self):
def test(format_code):
col = fits.Column(name='QUAL_SPE', format=format_code,
array=[[0] * 1571] * 225)
tb_hdu = fits.BinTableHDU.from_columns([col])
pri_hdu = fits.PrimaryHDU()
hdu_list = fits.HDUList([pri_hdu, tb_hdu])
with ignore_warnings():
hdu_list.writeto(self.temp('toto.fits'), overwrite=True)
with fits.open(self.temp('toto.fits')) as toto:
q = toto[1].data.field('QUAL_SPE')
assert (q[0][4:8] ==
np.array([0, 0, 0, 0], dtype=np.uint8)).all()
assert toto[1].columns[0].format.endswith('J(1571)')
for code in ('PJ()', 'QJ()'):
> test(code)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2638:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:2635: in test
assert toto[1].columns[0].format.endswith('J(1571)')
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____ TestVLATables.test_variable_length_table_format_pd_from_object_array _____
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x00000000210851d8>
def test_variable_length_table_format_pd_from_object_array(self):
def test(format_code):
a = np.array([np.array([7.2e-20, 7.3e-20]), np.array([0.0]),
np.array([0.0])], 'O')
acol = fits.Column(name='testa', format=format_code, array=a)
tbhdu = fits.BinTableHDU.from_columns([acol])
with ignore_warnings():
tbhdu.writeto(self.temp('newtable.fits'), overwrite=True)
with fits.open(self.temp('newtable.fits')) as tbhdu1:
assert tbhdu1[1].columns[0].format.endswith('D(2)')
for j in range(3):
for i in range(len(a[j])):
assert tbhdu1[1].data.field(0)[j][i] == a[j][i]
for code in ('PD()', 'QD()'):
> test(code)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2677:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:2674: in test
assert tbhdu1[1].data.field(0)[j][i] == a[j][i]
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestVLATables.test_variable_length_table_format_pd_from_list _________
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x0000000023902218>
def test_variable_length_table_format_pd_from_list(self):
def test(format_code):
a = [np.array([7.2e-20, 7.3e-20]), np.array([0.0]),
np.array([0.0])]
acol = fits.Column(name='testa', format=format_code, array=a)
tbhdu = fits.BinTableHDU.from_columns([acol])
with ignore_warnings():
tbhdu.writeto(self.temp('newtable.fits'), overwrite=True)
with fits.open(self.temp('newtable.fits')) as tbhdu1:
assert tbhdu1[1].columns[0].format.endswith('D(2)')
for j in range(3):
for i in range(len(a[j])):
assert tbhdu1[1].data.field(0)[j][i] == a[j][i]
for code in ('PD()', 'QD()'):
> test(code)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2695:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:2692: in test
assert tbhdu1[1].data.field(0)[j][i] == a[j][i]
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____ TestVLATables.test_variable_length_table_format_pa_from_object_array _____
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x000000000bde9398>
def test_variable_length_table_format_pa_from_object_array(self):
def test(format_code):
a = np.array([np.array(['a', 'b', 'c']), np.array(['d', 'e']),
np.array(['f'])], 'O')
acol = fits.Column(name='testa', format=format_code, array=a)
tbhdu = fits.BinTableHDU.from_columns([acol])
with ignore_warnings():
tbhdu.writeto(self.temp('newtable.fits'), overwrite=True)
with fits.open(self.temp('newtable.fits')) as hdul:
assert hdul[1].columns[0].format.endswith('A(3)')
for j in range(3):
for i in range(len(a[j])):
assert hdul[1].data.field(0)[j][i] == a[j][i]
for code in ('PA()', 'QA()'):
> test(code)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2713:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:2710: in test
assert hdul[1].data.field(0)[j][i] == a[j][i]
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________ TestVLATables.test_variable_length_table_format_pa_from_list _________
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x000000001f1428a8>
def test_variable_length_table_format_pa_from_list(self):
def test(format_code):
a = ['a', 'ab', 'abc']
acol = fits.Column(name='testa', format=format_code, array=a)
tbhdu = fits.BinTableHDU.from_columns([acol])
with ignore_warnings():
tbhdu.writeto(self.temp('newtable.fits'), overwrite=True)
with fits.open(self.temp('newtable.fits')) as hdul:
assert hdul[1].columns[0].format.endswith('A(3)')
for j in range(3):
for i in range(len(a[j])):
assert hdul[1].data.field(0)[j][i] == a[j][i]
for code in ('PA()', 'QA()'):
> test(code)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2730:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:2727: in test
assert hdul[1].data.field(0)[j][i] == a[j][i]
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________________ TestVLATables.test_getdata_vla ________________________
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x000000000c0aa9f8>
def test_getdata_vla(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/200"""
def test(format_code):
col = fits.Column(name='QUAL_SPE', format=format_code,
array=[np.arange(1572)] * 225)
tb_hdu = fits.BinTableHDU.from_columns([col])
pri_hdu = fits.PrimaryHDU()
hdu_list = fits.HDUList([pri_hdu, tb_hdu])
with ignore_warnings():
hdu_list.writeto(self.temp('toto.fits'), overwrite=True)
data = fits.getdata(self.temp('toto.fits'))
# Need to compare to the original data row by row since the FITS_rec
# returns an array of _VLA objects
for row_a, row_b in zip(data['QUAL_SPE'], col.array):
assert (row_a == row_b).all()
for code in ('PJ()', 'QJ()'):
> test(code)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2752:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/tests/test_table.py:2744: in test
data = fits.getdata(self.temp('toto.fits'))
pypy/site-packages/astropy/io/fits/convenience.py:204: in getdata
hdulist.close(closed=closed)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________________ TestVLATables.test_copy_vla __________________________
self = <astropy.io.fits.tests.test_table.TestVLATables object at 0x00000000119d5d00>
def test_copy_vla(self):
"""
Regression test for https://github.com/spacetelescope/PyFITS/issues/47
"""
# Make a file containing a couple of VLA tables
arr1 = [np.arange(n + 1) for n in range(255)]
arr2 = [np.arange(255, 256 + n) for n in range(255)]
# A dummy non-VLA column needed to reproduce issue #47
c = fits.Column('test', format='J', array=np.arange(255))
c1 = fits.Column('A', format='PJ', array=arr1)
c2 = fits.Column('B', format='PJ', array=arr2)
t1 = fits.BinTableHDU.from_columns([c, c1])
t2 = fits.BinTableHDU.from_columns([c, c2])
hdul = fits.HDUList([fits.PrimaryHDU(), t1, t2])
hdul.writeto(self.temp('test.fits'), overwrite=True)
# Just test that the test file wrote out correctly
with fits.open(self.temp('test.fits')) as h:
assert h[1].header['TFORM2'] == 'PJ(255)'
assert h[2].header['TFORM2'] == 'PJ(255)'
assert comparerecords(h[1].data, t1.data)
> assert comparerecords(h[2].data, t2.data)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2778:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ TestColumnFunctions.test_zero_precision_float_column _____________
self = <astropy.io.fits.tests.test_table.TestColumnFunctions object at 0x00000000128703d8>
def test_zero_precision_float_column(self):
"""
Regression test for https://github.com/astropy/astropy/issues/3422
"""
c = fits.Column('TEST', 'F5.0', array=[1.1, 2.2, 3.3])
# The decimal places will be clipped
t = fits.TableHDU.from_columns([c])
t.writeto(self.temp('test.fits'))
with fits.open(self.temp('test.fits')) as hdul:
assert hdul[1].header['TFORM1'] == 'F5.0'
assert hdul[1].data['TEST'].dtype == np.dtype('float64')
assert np.all(hdul[1].data['TEST'] == [1.0, 2.0, 3.0])
# Check how the raw data looks
raw = np.rec.recarray.field(hdul[1].data, 'TEST')
> assert raw.tostring() == b' 1. 2. 3.'
pypy/site-packages/astropy/io/fits/tests/test_table.py:2913:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________ TestColumnFunctions.test_pickle ________________________
self = <astropy.io.fits.tests.test_table.TestColumnFunctions object at 0x000000002234b248>
def test_pickle(self):
"""
Regression test for https://github.com/astropy/astropy/issues/1597
Tests for pickling FITS_rec objects
"""
# open existing FITS tables (images pickle by default, no test needed):
with fits.open(self.data('tb.fits')) as btb:
# Test column array is delayed and can pickle
assert isinstance(btb[1].columns._arrays[0], Delayed)
btb_pd = pickle.dumps(btb[1].data)
btb_pl = pickle.loads(btb_pd)
# It should not be delayed any more
assert not isinstance(btb[1].columns._arrays[0], Delayed)
> assert comparerecords(btb_pl, btb[1].data)
pypy/site-packages/astropy/io/fits/tests/test_table.py:2956:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________________________ test_empty_table _______________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_empty_table0')
def test_empty_table(tmpdir):
ofile = str(tmpdir.join('emptytable.fits'))
hdu = fits.BinTableHDU(header=None, data=None, name='TEST')
hdu.writeto(ofile)
with fits.open(ofile) as hdul:
> assert hdul['TEST'].data.size == 0
pypy/site-packages/astropy/io/fits/tests/test_table.py:3279:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestUintFunctions.test_uint[u2-False] _____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x0000000023961c20>
utype = 'u2', compressed = False
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002391f328>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000002391f328>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x0000000023961c20>
utype = 'u2', compressed = False
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestUintFunctions.test_uint[u4-False] _____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x00000000149eb6a8>
utype = 'u4', compressed = False
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000013c80de8>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000013c80de8>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x00000000149eb6a8>
utype = 'u4', compressed = False
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ TestUintFunctions.test_uint[u8-False] _____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x0000000009452250>
utype = 'u8', compressed = False
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000006f81b40>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x0000000006f81b40>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x0000000009452250>
utype = 'u8', compressed = False
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestUintFunctions.test_uint[u2-True] _____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x0000000022d676e0>
utype = 'u2', compressed = True
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001b18b2f0>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x000000001b18a790>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000001b18b2f0>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x000000001b18a790>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x0000000022d676e0>
utype = 'u2', compressed = True
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________ TestUintFunctions.test_uint[u4-True] _____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x000000001aeb0a30>
utype = 'u4', compressed = True
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000d5413d0>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x000000000d540678>]
type = None, value = None, traceback = None
def __exit__(self, type, value, traceback):
> self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000d5413d0>, <astropy.io.fits.hdu.compressed.CompImageHDU object at 0x000000000d540678>]
output_verify = 'exception', verbose = False, closed = True
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.
"""
try:
if (self._file and self._file.mode in ('append', 'update')
and not self._file.closed):
self.flush(output_verify=output_verify, verbose=verbose)
finally:
if self._file and closed and hasattr(self._file, 'close'):
> self._file.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>
def close(self):
"""
Close the 'physical' FITS file.
"""
if hasattr(self._file, 'close'):
self._file.close()
> self._maybe_close_mmap()
pypy/site-packages/astropy/io/fits/file.py:413:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
During handling of the above exception, another exception occurred:
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x000000001aeb0a30>
utype = 'u4', compressed = True
@pytest.mark.parametrize(('utype', 'compressed'),
[('u2', False), ('u4', False), ('u8', False), ('u2', True),
('u4', True)]) # ,('u8',True)])
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
> assert (sec == d1[:1]).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestUintFunctions.test_uint_columns[u2] ____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x00000000067fb1d8>
utype = 'u2'
@pytest.mark.parametrize('utype', ('u2', 'u4', 'u8'))
def test_uint_columns(self, utype):
"""Test basic functionality of tables with columns containing
pseudo-unsigned integers. See
https://github.com/astropy/astropy/pull/906
"""
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
bzero = self.utype_map[utype](2**(bits-1))
one = self.utype_map[utype](1)
u0 = np.arange(bits+1, dtype=self.utype_map[utype])
u = 2**u0 - one
if bits == 64:
u[63] = bzero - one
u[64] = u[63] + u[63] + one
uu = (u - bzero).view(self.itype_map[utype])
# Construct a table from explicit column
col = fits.Column(name=utype, array=u,
format=self.format_map[utype], bzero=bzero)
table = fits.BinTableHDU.from_columns([col])
assert (table.data[utype] == u).all()
# This used to be table.data.base, but now after adding a table to
# a BinTableHDU it gets stored as a view of the original table,
# even if the original was already a FITS_rec. So now we need
# table.data.base.base
assert (table.data.base.base[utype] == uu).all()
hdu0 = fits.PrimaryHDU()
hdulist = fits.HDUList([hdu0, table])
with ignore_warnings():
hdulist.writeto(self.temp('tempfile.fits'), overwrite=True)
# Test write of unsigned int
del hdulist
with fits.open(self.temp('tempfile.fits'), uint=True) as hdulist2:
hdudata = hdulist2[1].data
assert (hdudata[utype] == u).all()
assert (hdudata[utype].dtype == self.utype_map[utype])
> assert (hdudata.base[utype] == uu).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:102:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestUintFunctions.test_uint_columns[u4] ____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x000000001812eb10>
utype = 'u4'
@pytest.mark.parametrize('utype', ('u2', 'u4', 'u8'))
def test_uint_columns(self, utype):
"""Test basic functionality of tables with columns containing
pseudo-unsigned integers. See
https://github.com/astropy/astropy/pull/906
"""
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
bzero = self.utype_map[utype](2**(bits-1))
one = self.utype_map[utype](1)
u0 = np.arange(bits+1, dtype=self.utype_map[utype])
u = 2**u0 - one
if bits == 64:
u[63] = bzero - one
u[64] = u[63] + u[63] + one
uu = (u - bzero).view(self.itype_map[utype])
# Construct a table from explicit column
col = fits.Column(name=utype, array=u,
format=self.format_map[utype], bzero=bzero)
table = fits.BinTableHDU.from_columns([col])
assert (table.data[utype] == u).all()
# This used to be table.data.base, but now after adding a table to
# a BinTableHDU it gets stored as a view of the original table,
# even if the original was already a FITS_rec. So now we need
# table.data.base.base
assert (table.data.base.base[utype] == uu).all()
hdu0 = fits.PrimaryHDU()
hdulist = fits.HDUList([hdu0, table])
with ignore_warnings():
hdulist.writeto(self.temp('tempfile.fits'), overwrite=True)
# Test write of unsigned int
del hdulist
with fits.open(self.temp('tempfile.fits'), uint=True) as hdulist2:
hdudata = hdulist2[1].data
assert (hdudata[utype] == u).all()
assert (hdudata[utype].dtype == self.utype_map[utype])
> assert (hdudata.base[utype] == uu).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:102:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ TestUintFunctions.test_uint_columns[u8] ____________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x000000000f204170>
utype = 'u8'
@pytest.mark.parametrize('utype', ('u2', 'u4', 'u8'))
def test_uint_columns(self, utype):
"""Test basic functionality of tables with columns containing
pseudo-unsigned integers. See
https://github.com/astropy/astropy/pull/906
"""
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
bzero = self.utype_map[utype](2**(bits-1))
one = self.utype_map[utype](1)
u0 = np.arange(bits+1, dtype=self.utype_map[utype])
u = 2**u0 - one
if bits == 64:
u[63] = bzero - one
u[64] = u[63] + u[63] + one
uu = (u - bzero).view(self.itype_map[utype])
# Construct a table from explicit column
col = fits.Column(name=utype, array=u,
format=self.format_map[utype], bzero=bzero)
table = fits.BinTableHDU.from_columns([col])
assert (table.data[utype] == u).all()
# This used to be table.data.base, but now after adding a table to
# a BinTableHDU it gets stored as a view of the original table,
# even if the original was already a FITS_rec. So now we need
# table.data.base.base
assert (table.data.base.base[utype] == uu).all()
hdu0 = fits.PrimaryHDU()
hdulist = fits.HDUList([hdu0, table])
with ignore_warnings():
hdulist.writeto(self.temp('tempfile.fits'), overwrite=True)
# Test write of unsigned int
del hdulist
with fits.open(self.temp('tempfile.fits'), uint=True) as hdulist2:
hdudata = hdulist2[1].data
assert (hdudata[utype] == u).all()
assert (hdudata[utype].dtype == self.utype_map[utype])
> assert (hdudata.base[utype] == uu).all()
pypy/site-packages/astropy/io/fits/tests/test_uint.py:102:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________________ TestUintFunctions.test_uint_slice _______________________
self = <astropy.io.fits.tests.test_uint.TestUintFunctions object at 0x00000000180d52b8>
def test_uint_slice(self):
"""
Fix for https://github.com/astropy/astropy/issues/5490
if data is sliced first, make sure the data is still converted as uint
"""
# create_data:
dataref = np.arange(2**16, dtype=np.uint16)
tbhdu = fits.BinTableHDU.from_columns([
fits.Column(name='a', format='I',
array=np.arange(2**16, dtype=np.int16)),
fits.Column(name='b', format='I', bscale=1, bzero=2**15,
array=dataref)
])
tbhdu.writeto(self.temp('test_scaled_slicing.fits'))
with fits.open(self.temp('test_scaled_slicing.fits')) as hdulist:
> data = hdulist[1].data
pypy/site-packages/astropy/io/fits/tests/test_uint.py:133:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________________ test_gzip_filehandles _____________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_gzip_filehandles0')
def test_gzip_filehandles(tmpdir):
votable = parse(get_pkg_data_filename('data/regression.xml'))
# W39: Bit values can not be masked
with pytest.warns(W39):
with open(str(tmpdir.join("regression.compressed.xml")), 'wb') as fd:
votable.to_xml(fd, compressed=True, _astropy_version="testing")
with open(str(tmpdir.join("regression.compressed.xml")), 'rb') as fd:
> votable = parse(fd)
pypy/site-packages/astropy/io/votable/tests/vo_test.py:840:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/utils/decorators.py:521: in wrapper
return function(*args, **kwargs)
pypy/site-packages/astropy/io/votable/table.py:167: in parse
config=config, pos=(1, 1)).parse(iterator, config)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <VOTABLE>... 0 tables ...</VOTABLE>
iterator = <astropy.utils.xml._iterparser.IterParser object at 0x00000000223fbbe0>
config = {'_current_table_number': 0, 'chunk_size': 256, 'columns': None, 'datatype_mapping': {}, ...}
def parse(self, iterator, config):
config['_current_table_number'] = 0
> for start, tag, data, pos in iterator:
E EOFError: Compressed file ended before the end-of-stream marker was reached
pypy/site-packages/astropy/io/votable/tree.py:3505: EOFError
__________________________ test_initialize_from_FITS ___________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_FITS0')
def test_initialize_from_FITS(tmpdir):
ccd_data = create_ccd_data()
hdu = fits.PrimaryHDU(ccd_data)
hdulist = fits.HDUList([hdu])
filename = tmpdir.join('afile.fits').strpath
hdulist.writeto(filename)
> cd = CCDData.read(filename, unit=u.electron)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:83:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
________________ test_initialize_from_fits_with_unit_in_header _________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_fits_with0')
def test_initialize_from_fits_with_unit_in_header(tmpdir):
fake_img = np.zeros([2, 2])
hdu = fits.PrimaryHDU(fake_img)
hdu.header['bunit'] = u.adu.to_string()
filename = tmpdir.join('afile.fits').strpath
hdu.writeto(filename)
> ccd = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:97:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________ test_initialize_from_fits_with_ADU_in_header _________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_fits_with1')
def test_initialize_from_fits_with_ADU_in_header(tmpdir):
fake_img = np.zeros([2, 2])
hdu = fits.PrimaryHDU(fake_img)
hdu.header['bunit'] = 'ADU'
filename = tmpdir.join('afile.fits').strpath
hdu.writeto(filename)
> ccd = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:112:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ test_initialize_from_fits_with_invalid_unit_in_header _____________
cls = <class 'astropy.units.format.generic.Generic'>
s = 'definetely-not-a-unit', debug = False
@classmethod
def _do_parse(cls, s, debug=False):
try:
# This is a short circuit for the case where the string
# is just a single unit name
> return cls._parse_unit(s, detailed_exception=False)
pypy/site-packages/astropy/units/format/generic.py:566:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.units.format.generic.Generic'>
s = 'definetely-not-a-unit', detailed_exception = False
@classmethod
def _parse_unit(cls, s, detailed_exception=True):
registry = core.get_current_unit_registry().registry
if s == '%':
return registry['percent']
if not _is_ascii(s):
if s[0] == '\N{MICRO SIGN}':
s = 'u' + s[1:]
if s[-1] == '\N{GREEK CAPITAL LETTER OMEGA}':
s = s[:-1] + 'Ohm'
elif s[-1] == '\N{LATIN CAPITAL LETTER A WITH RING ABOVE}':
s = s[:-1] + 'Angstrom'
if s in registry:
return registry[s]
if detailed_exception:
raise ValueError(
'{} is not a valid unit. {}'.format(
s, did_you_mean(s, registry)))
else:
> raise ValueError()
E ValueError
pypy/site-packages/astropy/units/format/generic.py:487: ValueError
During handling of the above exception, another exception occurred:
cls = <class 'astropy.units.format.generic.Generic'>
t = LexToken(UNIT,'definetely',1,0)
@classmethod
def _get_unit(cls, t):
try:
> return cls._parse_unit(t.value)
pypy/site-packages/astropy/units/format/generic.py:459:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.units.format.generic.Generic'>, s = 'definetely'
detailed_exception = True
@classmethod
def _parse_unit(cls, s, detailed_exception=True):
registry = core.get_current_unit_registry().registry
if s == '%':
return registry['percent']
if not _is_ascii(s):
if s[0] == '\N{MICRO SIGN}':
s = 'u' + s[1:]
if s[-1] == '\N{GREEK CAPITAL LETTER OMEGA}':
s = s[:-1] + 'Ohm'
elif s[-1] == '\N{LATIN CAPITAL LETTER A WITH RING ABOVE}':
s = s[:-1] + 'Angstrom'
if s in registry:
return registry[s]
if detailed_exception:
raise ValueError(
'{} is not a valid unit. {}'.format(
> s, did_you_mean(s, registry)))
E ValueError: definetely is not a valid unit.
pypy/site-packages/astropy/units/format/generic.py:485: ValueError
During handling of the above exception, another exception occurred:
self = <class 'astropy.units.core.Unit'>, s = 'definetely-not-a-unit'
represents = None, format = <class 'astropy.units.format.generic.Generic'>
namespace = None, doc = None, parse_strict = 'raise'
def __call__(self, s, represents=None, format=None, namespace=None,
doc=None, parse_strict='raise'):
# Short-circuit if we're already a unit
if hasattr(s, '_get_physical_type_id'):
return s
# turn possible Quantity input for s or represents into a Unit
from .quantity import Quantity
if isinstance(represents, Quantity):
if is_effectively_unity(represents.value):
represents = represents.unit
else:
represents = CompositeUnit(represents.value *
represents.unit.scale,
bases=represents.unit.bases,
powers=represents.unit.powers,
_error_check=False)
if isinstance(s, Quantity):
if is_effectively_unity(s.value):
s = s.unit
else:
s = CompositeUnit(s.value * s.unit.scale,
bases=s.unit.bases,
powers=s.unit.powers,
_error_check=False)
# now decide what we really need to do; define derived Unit?
if isinstance(represents, UnitBase):
# This has the effect of calling the real __new__ and
# __init__ on the Unit class.
return super().__call__(
s, represents, format=format, namespace=namespace, doc=doc)
# or interpret a Quantity (now became unit), string or number?
if isinstance(s, UnitBase):
return s
elif isinstance(s, (bytes, str)):
if len(s.strip()) == 0:
# Return the NULL unit
return dimensionless_unscaled
if format is None:
format = unit_format.Generic
f = unit_format.get_format(format)
if isinstance(s, bytes):
s = s.decode('ascii')
try:
> return f.parse(s)
pypy/site-packages/astropy/units/core.py:1854:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.units.format.generic.Generic'>
s = 'definetely-not-a-unit', debug = False
@classmethod
def parse(cls, s, debug=False):
if not isinstance(s, str):
s = s.decode('ascii')
elif not _is_ascii(s):
# common normalization of unicode strings to avoid
# having to deal with multiple representations of
# the same character. This normalizes to "composed" form
# and will e.g. convert OHM SIGN to GREEK CAPITAL LETTER OMEGA
s = unicodedata.normalize('NFC', s)
# Translate some basic unicode items that we'd like to support on
# input but are not standard.
s = s.translate(cls._translations)
# TODO: might the below be better done in the parser/lexer?
# Translate superscripts to parenthesized numbers; this ensures
# that mixes of superscripts and regular numbers fail.
s = cls._regex_superscript.sub(cls._convert_superscript, s)
# Translate possible degrees.
s = cls._regex_deg.sub(cls._convert_deg, s)
> result = cls._do_parse(s, debug=debug)
pypy/site-packages/astropy/units/format/generic.py:551:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.units.format.generic.Generic'>
s = 'definetely-not-a-unit', debug = False
@classmethod
def _do_parse(cls, s, debug=False):
try:
# This is a short circuit for the case where the string
# is just a single unit name
return cls._parse_unit(s, detailed_exception=False)
except ValueError as e:
try:
> return cls._parser.parse(s, lexer=cls._lexer, debug=debug)
pypy/site-packages/astropy/units/format/generic.py:569:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.extern.ply.yacc.LRParser object at 0x00007f587b987cc8>
input = 'definetely-not-a-unit'
lexer = <astropy.extern.ply.lex.Lexer object at 0x00007f587b9866e8>
debug = False, tracking = False, tokenfunc = None
def parse(self, input=None, lexer=None, debug=False, tracking=False, tokenfunc=None):
if debug or yaccdevel:
if isinstance(debug, int):
debug = PlyLogger(sys.stderr)
return self.parsedebug(input, lexer, debug, tracking, tokenfunc)
elif tracking:
return self.parseopt(input, lexer, debug, tracking, tokenfunc)
else:
> return self.parseopt_notrack(input, lexer, debug, tracking, tokenfunc)
pypy/site-packages/astropy/extern/ply/yacc.py:331:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.extern.ply.yacc.LRParser object at 0x00007f587b987cc8>
input = 'definetely-not-a-unit'
lexer = <astropy.extern.ply.lex.Lexer object at 0x00007f587b9866e8>
debug = False, tracking = False, tokenfunc = None
def parseopt_notrack(self, input=None, lexer=None, debug=False, tracking=False, tokenfunc=None):
#--! parseopt-notrack-start
lookahead = None # Current lookahead symbol
lookaheadstack = [] # Stack of lookahead symbols
actions = self.action # Local reference to action table (to avoid lookup on self.)
goto = self.goto # Local reference to goto table (to avoid lookup on self.)
prod = self.productions # Local reference to production list (to avoid lookup on self.)
defaulted_states = self.defaulted_states # Local reference to defaulted states
pslice = YaccProduction(None) # Production object passed to grammar rules
errorcount = 0 # Used during error recovery
# If no lexer was given, we will try to use the lex module
if not lexer:
from . import lex
lexer = lex.lexer
# Set up the lexer and parser objects on pslice
pslice.lexer = lexer
pslice.parser = self
# If input was supplied, pass to lexer
if input is not None:
lexer.input(input)
if tokenfunc is None:
# Tokenize function
get_token = lexer.token
else:
get_token = tokenfunc
# Set the parser() token method (sometimes used in error recovery)
self.token = get_token
# Set up the state and symbol stacks
statestack = [] # Stack of parsing states
self.statestack = statestack
symstack = [] # Stack of grammar symbols
self.symstack = symstack
pslice.stack = symstack # Put in the production
errtoken = None # Err token
# The start state is assumed to be (0,$end)
statestack.append(0)
sym = YaccSymbol()
sym.type = '$end'
symstack.append(sym)
state = 0
while True:
# Get the next symbol on the input. If a lookahead symbol
# is already set, we just use that. Otherwise, we'll pull
# the next token off of the lookaheadstack or from the lexer
if state not in defaulted_states:
if not lookahead:
if not lookaheadstack:
> lookahead = get_token() # Get the next token
pypy/site-packages/astropy/extern/ply/yacc.py:1061:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.extern.ply.lex.Lexer object at 0x00007f587b9866e8>
def token(self):
# Make local copies of frequently referenced attributes
lexpos = self.lexpos
lexlen = self.lexlen
lexignore = self.lexignore
lexdata = self.lexdata
while lexpos < lexlen:
# This code provides some short-circuit code for whitespace, tabs, and other ignored characters
if lexdata[lexpos] in lexignore:
lexpos += 1
continue
# Look for a regular expression match
for lexre, lexindexfunc in self.lexre:
m = lexre.match(lexdata, lexpos)
if not m:
continue
# Create a token for return
tok = LexToken()
tok.value = m.group()
tok.lineno = self.lineno
tok.lexpos = lexpos
i = m.lastindex
func, tok.type = lexindexfunc[i]
if not func:
# If no token type was set, it's an ignored token
if tok.type:
self.lexpos = m.end()
return tok
else:
lexpos = m.end()
break
lexpos = m.end()
# If token is processed by a function, call it
tok.lexer = self # Set additional attributes useful in token rules
self.lexmatch = m
self.lexpos = lexpos
> newtok = func(tok)
pypy/site-packages/astropy/extern/ply/lex.py:350:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
t = LexToken(UNIT,'definetely',1,0)
def t_UNIT(t):
"%|([YZEPTGMkhdcmu\N{MICRO SIGN}npfazy]?'((?!\\d)\\w)+')|((?!\\d)\\w)+"
> t.value = cls._get_unit(t)
pypy/site-packages/astropy/units/format/generic.py:165:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'astropy.units.format.generic.Generic'>
t = LexToken(UNIT,'definetely',1,0)
@classmethod
def _get_unit(cls, t):
try:
return cls._parse_unit(t.value)
except ValueError as e:
raise ValueError(
"At col {}, {}".format(
> t.lexpos, str(e)))
E ValueError: At col 0, definetely is not a valid unit.
pypy/site-packages/astropy/units/format/generic.py:463: ValueError
During handling of the above exception, another exception occurred:
filename = <_io.FileIO [closed]>, hdu = 0, unit = None
hdu_uncertainty = 'UNCERT', hdu_mask = 'MASK', hdu_flags = None
key_uncertainty_type = 'UTYPE', kwd = {}
unsupport_open_keywords = {'do_not_scale_image_data': 'Image data must be scaled.', 'scale_back': 'Scale information is not preserved.'}
key = 'scale_back', msg = 'Scale information is not preserved.'
hdus = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000dd96ad8>]
hdr = SIMPLE = T / conforms to FITS standard
BITPIX = -64 / arra...
BUNIT = 'definetely-not-a-unit'
def fits_ccddata_reader(filename, hdu=0, unit=None, hdu_uncertainty='UNCERT',
hdu_mask='MASK', hdu_flags=None,
key_uncertainty_type='UTYPE', **kwd):
"""
Generate a CCDData object from a FITS file.
Parameters
----------
filename : str
Name of fits file.
hdu : int, optional
FITS extension from which CCDData should be initialized. If zero and
and no data in the primary extension, it will search for the first
extension with data. The header will be added to the primary header.
Default is ``0``.
unit : `~astropy.units.Unit`, optional
Units of the image data. If this argument is provided and there is a
unit for the image in the FITS header (the keyword ``BUNIT`` is used
as the unit, if present), this argument is used for the unit.
Default is ``None``.
hdu_uncertainty : str or None, optional
FITS extension from which the uncertainty should be initialized. If the
extension does not exist the uncertainty of the CCDData is ``None``.
Default is ``'UNCERT'``.
hdu_mask : str or None, optional
FITS extension from which the mask should be initialized. If the
extension does not exist the mask of the CCDData is ``None``.
Default is ``'MASK'``.
hdu_flags : str or None, optional
Currently not implemented.
Default is ``None``.
key_uncertainty_type : str, optional
The header key name where the class name of the uncertainty is stored
in the hdu of the uncertainty (if any).
Default is ``UTYPE``.
.. versionadded:: 3.1
kwd :
Any additional keyword parameters are passed through to the FITS reader
in :mod:`astropy.io.fits`; see Notes for additional discussion.
Notes
-----
FITS files that contained scaled data (e.g. unsigned integer images) will
be scaled and the keywords used to manage scaled data in
:mod:`astropy.io.fits` are disabled.
"""
unsupport_open_keywords = {
'do_not_scale_image_data': 'Image data must be scaled.',
'scale_back': 'Scale information is not preserved.'
}
for key, msg in unsupport_open_keywords.items():
if key in kwd:
prefix = f'unsupported keyword: {key}.'
raise TypeError(' '.join([prefix, msg]))
with fits.open(filename, **kwd) as hdus:
hdr = hdus[hdu].header
if hdu_uncertainty is not None and hdu_uncertainty in hdus:
unc_hdu = hdus[hdu_uncertainty]
stored_unc_name = unc_hdu.header.get(key_uncertainty_type, 'None')
# For compatibility reasons the default is standard deviation
# uncertainty because files could have been created before the
# uncertainty type was stored in the header.
unc_type = _unc_name_to_cls.get(stored_unc_name, StdDevUncertainty)
uncertainty = unc_type(unc_hdu.data)
else:
uncertainty = None
if hdu_mask is not None and hdu_mask in hdus:
# Mask is saved as uint but we want it to be boolean.
mask = hdus[hdu_mask].data.astype(np.bool_)
else:
mask = None
if hdu_flags is not None and hdu_flags in hdus:
raise NotImplementedError('loading flags is currently not '
'supported.')
# search for the first instance with data if
# the primary header is empty.
if hdu == 0 and hdus[hdu].data is None:
for i in range(len(hdus)):
if (hdus.info(hdu)[i][3] == 'ImageHDU' and
hdus.fileinfo(i)['datSpan'] > 0):
hdu = i
comb_hdr = hdus[hdu].header.copy()
# Add header values from the primary header that aren't
# present in the extension header.
comb_hdr.extend(hdr, unique=True)
hdr = comb_hdr
log.info("first HDU with data is extension "
"{}.".format(hdu))
break
if 'bunit' in hdr:
fits_unit_string = hdr['bunit']
# patch to handle FITS files using ADU for the unit instead of the
# standard version of 'adu'
if fits_unit_string.strip().lower() == 'adu':
fits_unit_string = fits_unit_string.lower()
else:
fits_unit_string = None
if fits_unit_string:
if unit is None:
# Convert the BUNIT header keyword to a unit and if that's not
# possible raise a meaningful error message.
try:
kifus = CCDData.known_invalid_fits_unit_strings
if fits_unit_string in kifus:
fits_unit_string = kifus[fits_unit_string]
> fits_unit_string = u.Unit(fits_unit_string)
pypy/site-packages/astropy/nddata/ccddata.py:648:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <class 'astropy.units.core.Unit'>, s = 'definetely-not-a-unit'
represents = None, format = <class 'astropy.units.format.generic.Generic'>
namespace = None, doc = None, parse_strict = 'raise'
def __call__(self, s, represents=None, format=None, namespace=None,
doc=None, parse_strict='raise'):
# Short-circuit if we're already a unit
if hasattr(s, '_get_physical_type_id'):
return s
# turn possible Quantity input for s or represents into a Unit
from .quantity import Quantity
if isinstance(represents, Quantity):
if is_effectively_unity(represents.value):
represents = represents.unit
else:
represents = CompositeUnit(represents.value *
represents.unit.scale,
bases=represents.unit.bases,
powers=represents.unit.powers,
_error_check=False)
if isinstance(s, Quantity):
if is_effectively_unity(s.value):
s = s.unit
else:
s = CompositeUnit(s.value * s.unit.scale,
bases=s.unit.bases,
powers=s.unit.powers,
_error_check=False)
# now decide what we really need to do; define derived Unit?
if isinstance(represents, UnitBase):
# This has the effect of calling the real __new__ and
# __init__ on the Unit class.
return super().__call__(
s, represents, format=format, namespace=namespace, doc=doc)
# or interpret a Quantity (now became unit), string or number?
if isinstance(s, UnitBase):
return s
elif isinstance(s, (bytes, str)):
if len(s.strip()) == 0:
# Return the NULL unit
return dimensionless_unscaled
if format is None:
format = unit_format.Generic
f = unit_format.get_format(format)
if isinstance(s, bytes):
s = s.decode('ascii')
try:
return f.parse(s)
except Exception as e:
if parse_strict == 'silent':
pass
else:
# Deliberately not issubclass here. Subclasses
# should use their name.
if f is not unit_format.Generic:
format_clause = f.name + ' '
else:
format_clause = ''
msg = ("'{}' did not parse as {}unit: {} "
"If this is meant to be a custom unit, "
"define it with 'u.def_unit'. To have it "
"recognized inside a file reader or other code, "
"enable it with 'u.add_enabled_units'. "
"For details, see "
"http://docs.astropy.org/en/latest/units/combining_and_defining.html"
.format(s, format_clause, str(e)))
if parse_strict == 'raise':
> raise ValueError(msg)
E ValueError: 'definetely-not-a-unit' did not parse as unit: At col 0, definetely is not a valid unit. If this is meant to be a custom unit, define it with 'u.def_unit'. To have it recognized inside a file reader or other code, enable it with 'u.add_enabled_units'. For details, see http://docs.astropy.org/en/latest/units/combining_and_defining.html
pypy/site-packages/astropy/units/core.py:1874: ValueError
During handling of the above exception, another exception occurred:
filename = <_io.FileIO [closed]>, hdu = 0, unit = None
hdu_uncertainty = 'UNCERT', hdu_mask = 'MASK', hdu_flags = None
key_uncertainty_type = 'UTYPE', kwd = {}
unsupport_open_keywords = {'do_not_scale_image_data': 'Image data must be scaled.', 'scale_back': 'Scale information is not preserved.'}
key = 'scale_back', msg = 'Scale information is not preserved.'
hdus = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000dd96ad8>]
hdr = SIMPLE = T / conforms to FITS standard
BITPIX = -64 / arra...
BUNIT = 'definetely-not-a-unit'
def fits_ccddata_reader(filename, hdu=0, unit=None, hdu_uncertainty='UNCERT',
hdu_mask='MASK', hdu_flags=None,
key_uncertainty_type='UTYPE', **kwd):
"""
Generate a CCDData object from a FITS file.
Parameters
----------
filename : str
Name of fits file.
hdu : int, optional
FITS extension from which CCDData should be initialized. If zero and
and no data in the primary extension, it will search for the first
extension with data. The header will be added to the primary header.
Default is ``0``.
unit : `~astropy.units.Unit`, optional
Units of the image data. If this argument is provided and there is a
unit for the image in the FITS header (the keyword ``BUNIT`` is used
as the unit, if present), this argument is used for the unit.
Default is ``None``.
hdu_uncertainty : str or None, optional
FITS extension from which the uncertainty should be initialized. If the
extension does not exist the uncertainty of the CCDData is ``None``.
Default is ``'UNCERT'``.
hdu_mask : str or None, optional
FITS extension from which the mask should be initialized. If the
extension does not exist the mask of the CCDData is ``None``.
Default is ``'MASK'``.
hdu_flags : str or None, optional
Currently not implemented.
Default is ``None``.
key_uncertainty_type : str, optional
The header key name where the class name of the uncertainty is stored
in the hdu of the uncertainty (if any).
Default is ``UTYPE``.
.. versionadded:: 3.1
kwd :
Any additional keyword parameters are passed through to the FITS reader
in :mod:`astropy.io.fits`; see Notes for additional discussion.
Notes
-----
FITS files that contained scaled data (e.g. unsigned integer images) will
be scaled and the keywords used to manage scaled data in
:mod:`astropy.io.fits` are disabled.
"""
unsupport_open_keywords = {
'do_not_scale_image_data': 'Image data must be scaled.',
'scale_back': 'Scale information is not preserved.'
}
for key, msg in unsupport_open_keywords.items():
if key in kwd:
prefix = f'unsupported keyword: {key}.'
raise TypeError(' '.join([prefix, msg]))
with fits.open(filename, **kwd) as hdus:
hdr = hdus[hdu].header
if hdu_uncertainty is not None and hdu_uncertainty in hdus:
unc_hdu = hdus[hdu_uncertainty]
stored_unc_name = unc_hdu.header.get(key_uncertainty_type, 'None')
# For compatibility reasons the default is standard deviation
# uncertainty because files could have been created before the
# uncertainty type was stored in the header.
unc_type = _unc_name_to_cls.get(stored_unc_name, StdDevUncertainty)
uncertainty = unc_type(unc_hdu.data)
else:
uncertainty = None
if hdu_mask is not None and hdu_mask in hdus:
# Mask is saved as uint but we want it to be boolean.
mask = hdus[hdu_mask].data.astype(np.bool_)
else:
mask = None
if hdu_flags is not None and hdu_flags in hdus:
raise NotImplementedError('loading flags is currently not '
'supported.')
# search for the first instance with data if
# the primary header is empty.
if hdu == 0 and hdus[hdu].data is None:
for i in range(len(hdus)):
if (hdus.info(hdu)[i][3] == 'ImageHDU' and
hdus.fileinfo(i)['datSpan'] > 0):
hdu = i
comb_hdr = hdus[hdu].header.copy()
# Add header values from the primary header that aren't
# present in the extension header.
comb_hdr.extend(hdr, unique=True)
hdr = comb_hdr
log.info("first HDU with data is extension "
"{}.".format(hdu))
break
if 'bunit' in hdr:
fits_unit_string = hdr['bunit']
# patch to handle FITS files using ADU for the unit instead of the
# standard version of 'adu'
if fits_unit_string.strip().lower() == 'adu':
fits_unit_string = fits_unit_string.lower()
else:
fits_unit_string = None
if fits_unit_string:
if unit is None:
# Convert the BUNIT header keyword to a unit and if that's not
# possible raise a meaningful error message.
try:
kifus = CCDData.known_invalid_fits_unit_strings
if fits_unit_string in kifus:
fits_unit_string = kifus[fits_unit_string]
fits_unit_string = u.Unit(fits_unit_string)
except ValueError:
raise ValueError(
'The Header value for the key BUNIT ({}) cannot be '
'interpreted as valid unit. To successfully read the '
'file as CCDData you can pass in a valid `unit` '
'argument explicitly or change the header of the FITS '
'file before reading it.'
> .format(fits_unit_string))
E ValueError: The Header value for the key BUNIT (definetely-not-a-unit) cannot be interpreted as valid unit. To successfully read the file as CCDData you can pass in a valid `unit` argument explicitly or change the header of the FITS file before reading it.
pypy/site-packages/astropy/nddata/ccddata.py:656: ValueError
During handling of the above exception, another exception occurred:
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_fits_with2')
def test_initialize_from_fits_with_invalid_unit_in_header(tmpdir):
hdu = fits.PrimaryHDU(np.ones((2, 2)))
hdu.header['bunit'] = 'definetely-not-a-unit'
filename = tmpdir.join('afile.fits').strpath
hdu.writeto(filename)
with pytest.raises(ValueError):
> CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______ test_initialize_from_fits_with_technically_invalid_but_not_really _______
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_fits_with3')
def test_initialize_from_fits_with_technically_invalid_but_not_really(tmpdir):
hdu = fits.PrimaryHDU(np.ones((2, 2)))
hdu.header['bunit'] = 'ELECTRONS/S'
filename = tmpdir.join('afile.fits').strpath
hdu.writeto(filename)
> ccd = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:131:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________ test_initialize_from_fits_with_data_in_different_extension __________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_fits_with4')
def test_initialize_from_fits_with_data_in_different_extension(tmpdir):
fake_img = np.arange(4).reshape(2, 2)
hdu1 = fits.PrimaryHDU()
hdu2 = fits.ImageHDU(fake_img)
hdus = fits.HDUList([hdu1, hdu2])
filename = tmpdir.join('afile.fits').strpath
hdus.writeto(filename)
with catch_warnings(FITSFixedWarning) as w:
> ccd = CCDData.read(filename, unit='adu')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:143:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
----------------------------- Captured stdout call -----------------------------
INFO: first HDU with data is extension 1. [astropy.nddata.ccddata]
------------------------------ Captured log call -------------------------------
INFO astropy:ccddata.py:628 first HDU with data is extension 1.
___________________ test_initialize_from_fits_with_extension ___________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_initialize_from_fits_with5')
def test_initialize_from_fits_with_extension(tmpdir):
fake_img1 = np.zeros([2, 2])
fake_img2 = np.arange(4).reshape(2, 2)
hdu0 = fits.PrimaryHDU()
hdu1 = fits.ImageHDU(fake_img1)
hdu2 = fits.ImageHDU(fake_img2)
hdus = fits.HDUList([hdu0, hdu1, hdu2])
filename = tmpdir.join('afile.fits').strpath
hdus.writeto(filename)
> ccd = CCDData.read(filename, hdu=2, unit='adu')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:160:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________________________ test_ccddata_writer ______________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_ccddata_writer0')
def test_ccddata_writer(tmpdir):
ccd_data = create_ccd_data()
filename = tmpdir.join('test.fits').strpath
ccd_data.write(filename)
> ccd_disk = CCDData.read(filename, unit=ccd_data.unit)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:192:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
----------------------------- Captured stdout call -----------------------------
INFO: using the unit adu passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]
------------------------------ Captured log call -------------------------------
INFO astropy:ccddata.py:660 using the unit adu passed to the FITS reader instead of the unit adu in the FITS file.
_________________________________ test_fromMEF _________________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_fromMEF0')
def test_fromMEF(tmpdir):
ccd_data = create_ccd_data()
hdu = fits.PrimaryHDU(ccd_data)
hdu2 = fits.PrimaryHDU(2 * ccd_data.data)
hdulist = fits.HDUList(hdu)
hdulist.append(hdu2)
filename = tmpdir.join('afile.fits').strpath
hdulist.writeto(filename)
# by default, we reading from the first extension
> cd = CCDData.read(filename, unit=u.electron)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:220:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
______________ test_history_preserved_if_metadata_is_fits_header _______________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_history_preserved_if_meta0')
def test_history_preserved_if_metadata_is_fits_header(tmpdir):
fake_img = np.zeros([2, 2])
hdu = fits.PrimaryHDU(fake_img)
hdu.header['history'] = 'one'
hdu.header['history'] = 'two'
hdu.header['history'] = 'three'
assert len(hdu.header['history']) == 3
tmp_file = tmpdir.join('temp.fits').strpath
hdu.writeto(tmp_file)
> ccd_read = CCDData.read(tmp_file, unit="adu")
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:571:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________ test_infol_logged_if_unit_in_fits_header ___________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_infol_logged_if_unit_in_f0')
def test_infol_logged_if_unit_in_fits_header(tmpdir):
ccd_data = create_ccd_data()
tmpfile = tmpdir.join('temp.fits')
ccd_data.write(tmpfile.strpath)
log.setLevel('INFO')
explicit_unit_name = "photon"
with log.log_to_list() as log_list:
> ccd_from_disk = CCDData.read(tmpfile.strpath, unit=explicit_unit_name)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:582:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
----------------------------- Captured stdout call -----------------------------
INFO: using the unit photon passed to the FITS reader instead of the unit adu in the FITS file. [astropy.nddata.ccddata]
------------------------------ Captured log call -------------------------------
INFO astropy:ccddata.py:660 using the unit photon passed to the FITS reader instead of the unit adu in the FITS file.
______________________________ test_wcs_attribute ______________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_wcs_attribute0')
def test_wcs_attribute(tmpdir):
"""
Check that WCS attribute gets added to header, and that if a CCDData
object is created from a FITS file with a header, and the WCS attribute
is modified, then the CCDData object is turned back into an hdu, the
WCS object overwrites the old WCS information in the header.
"""
ccd_data = create_ccd_data()
tmpfile = tmpdir.join('temp.fits')
# This wcs example is taken from the astropy.wcs docs.
wcs = WCS(naxis=2)
wcs.wcs.crpix = np.array(ccd_data.shape) / 2
wcs.wcs.cdelt = np.array([-0.066667, 0.066667])
wcs.wcs.crval = [0, -90]
wcs.wcs.ctype = ["RA---AIR", "DEC--AIR"]
wcs.wcs.set_pv([(2, 1, 45.0)])
ccd_data.header = ccd_data.to_hdu()[0].header
ccd_data.header.extend(wcs.to_header(), useblanks=False)
ccd_data.write(tmpfile.strpath)
# Get the header length after it has been extended by the WCS keywords
original_header_length = len(ccd_data.header)
> ccd_new = CCDData.read(tmpfile.strpath)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:609:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ test_wcs_keywords_removed_from_header _____________________
def test_wcs_keywords_removed_from_header():
"""
Test, for the file included with the nddata tests, that WCS keywords are
properly removed from header.
"""
from astropy.nddata.ccddata import _KEEP_THESE_KEYWORDS_IN_HEADER
keepers = set(_KEEP_THESE_KEYWORDS_IN_HEADER)
data_file = get_pkg_data_filename('data/sip-wcs.fits')
> ccd = CCDData.read(data_file)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:655:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__________________ test_wcs_SIP_coefficient_keywords_removed ___________________
def test_wcs_SIP_coefficient_keywords_removed():
# If SIP polynomials are present, check that no more polynomial
# coefficients remain in the header. See #8598
# The SIP paper is ambiguous as to whether keywords like
# A_0_0 can appear in the header for a 2nd order or higher
# polynomial. The paper clearly says that the corrections
# are only for quadratic or higher order, so A_0_0 and the like
# should be zero if they are present, but they apparently can be
# there (or at least astrometry.net produces them).
# astropy WCS does not write those coefficients, so they were
# not being removed from the header even though they are WCS-related.
data_file = get_pkg_data_filename('data/sip-wcs.fits')
test_keys = ['A_0_0', 'B_0_1']
# Make sure the keywords added to this file for testing are there
with fits.open(data_file) as hdu:
for key in test_keys:
assert key in hdu[0].header
> ccd = CCDData.read(data_file)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:690:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________________ test_read_wcs_not_creatable __________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_read_wcs_not_creatable0')
def test_read_wcs_not_creatable(tmpdir):
# The following Header can't be converted to a WCS object. See also #6499.
hdr_txt_example_WCS = textwrap.dedent('''
SIMPLE = T / Fits standard
BITPIX = 16 / Bits per pixel
NAXIS = 2 / Number of axes
NAXIS1 = 1104 / Axis length
NAXIS2 = 4241 / Axis length
CRVAL1 = 164.98110962 / Physical value of the reference pixel X
CRVAL2 = 44.34089279 / Physical value of the reference pixel Y
CRPIX1 = -34.0 / Reference pixel in X (pixel)
CRPIX2 = 2041.0 / Reference pixel in Y (pixel)
CDELT1 = 0.10380000 / X Scale projected on detector (#/pix)
CDELT2 = 0.10380000 / Y Scale projected on detector (#/pix)
CTYPE1 = 'RA---TAN' / Pixel coordinate system
CTYPE2 = 'WAVELENGTH' / Pixel coordinate system
CUNIT1 = 'degree ' / Units used in both CRVAL1 and CDELT1
CUNIT2 = 'nm ' / Units used in both CRVAL2 and CDELT2
CD1_1 = 0.20760000 / Pixel Coordinate translation matrix
CD1_2 = 0.00000000 / Pixel Coordinate translation matrix
CD2_1 = 0.00000000 / Pixel Coordinate translation matrix
CD2_2 = 0.10380000 / Pixel Coordinate translation matrix
C2YPE1 = 'RA---TAN' / Pixel coordinate system
C2YPE2 = 'DEC--TAN' / Pixel coordinate system
C2NIT1 = 'degree ' / Units used in both C2VAL1 and C2ELT1
C2NIT2 = 'degree ' / Units used in both C2VAL2 and C2ELT2
RADECSYS= 'FK5 ' / The equatorial coordinate system
''')
with catch_warnings(FITSFixedWarning):
hdr = fits.Header.fromstring(hdr_txt_example_WCS, sep='\n')
hdul = fits.HDUList([fits.PrimaryHDU(np.ones((4241, 1104)), header=hdr)])
filename = tmpdir.join('afile.fits').strpath
hdul.writeto(filename)
# The hdr cannot be converted to a WCS object because of an
# InconsistentAxisTypesError but it should still open the file
> ccd = CCDData.read(filename, unit='adu')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:790:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
----------------------------- Captured stdout call -----------------------------
INFO: An exception happened while extracting WCS informations from the Header.
InconsistentAxisTypesError: ERROR 4 in wcs_types() at line 2707 of file cextern/wcslib/C/wcs.c:
Unmatched celestial axes.
[astropy.nddata.ccddata]
------------------------------ Captured log call -------------------------------
INFO astropy:ccddata.py:480 An exception happened while extracting WCS informations from the Header.
InconsistentAxisTypesError: ERROR 4 in wcs_types() at line 2707 of file cextern/wcslib/C/wcs.c:
Unmatched celestial axes.
____________________________ test_wcs_sip_handling _____________________________
def test_wcs_sip_handling():
"""
Check whether the ctypes RA---TAN-SIP and DEC--TAN-SIP survive
a roundtrip unchanged.
"""
data_file = get_pkg_data_filename('data/sip-wcs.fits')
def check_wcs_ctypes(header):
expected_wcs_ctypes = {
'CTYPE1': 'RA---TAN-SIP',
'CTYPE2': 'DEC--TAN-SIP'
}
return [header[k] == v for k, v in expected_wcs_ctypes.items()]
> ccd_original = CCDData.read(data_file)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:836:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_______________ test_write_read_multiextensionfits_mask_default ________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension0')
def test_write_read_multiextensionfits_mask_default(tmpdir):
# Test that if a mask is present the mask is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.mask = ccd_data.data > 10
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename)
> ccd_after = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:875:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
__ test_write_read_multiextensionfits_uncertainty_default[StdDevUncertainty] ___
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension1')
uncertainty_type = <class 'astropy.nddata.nduncertainty.StdDevUncertainty'>
@pytest.mark.parametrize(
'uncertainty_type',
[StdDevUncertainty, VarianceUncertainty, InverseVariance])
def test_write_read_multiextensionfits_uncertainty_default(
tmpdir, uncertainty_type):
# Test that if a uncertainty is present it is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.uncertainty = uncertainty_type(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename)
> ccd_after = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:890:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ test_write_read_multiextensionfits_uncertainty_default[VarianceUncertainty] __
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension2')
uncertainty_type = <class 'astropy.nddata.nduncertainty.VarianceUncertainty'>
@pytest.mark.parametrize(
'uncertainty_type',
[StdDevUncertainty, VarianceUncertainty, InverseVariance])
def test_write_read_multiextensionfits_uncertainty_default(
tmpdir, uncertainty_type):
# Test that if a uncertainty is present it is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.uncertainty = uncertainty_type(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename)
> ccd_after = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:890:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___ test_write_read_multiextensionfits_uncertainty_default[InverseVariance] ____
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension3')
uncertainty_type = <class 'astropy.nddata.nduncertainty.InverseVariance'>
@pytest.mark.parametrize(
'uncertainty_type',
[StdDevUncertainty, VarianceUncertainty, InverseVariance])
def test_write_read_multiextensionfits_uncertainty_default(
tmpdir, uncertainty_type):
# Test that if a uncertainty is present it is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.uncertainty = uncertainty_type(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename)
> ccd_after = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:890:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ test_write_read_multiextensionfits_uncertainty_different_uncertainty_key[StdDevUncertainty] _
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension4')
uncertainty_type = <class 'astropy.nddata.nduncertainty.StdDevUncertainty'>
@pytest.mark.parametrize(
'uncertainty_type',
[StdDevUncertainty, VarianceUncertainty, InverseVariance])
def test_write_read_multiextensionfits_uncertainty_different_uncertainty_key(
tmpdir, uncertainty_type):
# Test that if a uncertainty is present it is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.uncertainty = uncertainty_type(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename, key_uncertainty_type='Blah')
> ccd_after = CCDData.read(filename, key_uncertainty_type='Blah')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:907:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ test_write_read_multiextensionfits_uncertainty_different_uncertainty_key[VarianceUncertainty] _
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension5')
uncertainty_type = <class 'astropy.nddata.nduncertainty.VarianceUncertainty'>
@pytest.mark.parametrize(
'uncertainty_type',
[StdDevUncertainty, VarianceUncertainty, InverseVariance])
def test_write_read_multiextensionfits_uncertainty_different_uncertainty_key(
tmpdir, uncertainty_type):
# Test that if a uncertainty is present it is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.uncertainty = uncertainty_type(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename, key_uncertainty_type='Blah')
> ccd_after = CCDData.read(filename, key_uncertainty_type='Blah')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:907:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_ test_write_read_multiextensionfits_uncertainty_different_uncertainty_key[InverseVariance] _
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension6')
uncertainty_type = <class 'astropy.nddata.nduncertainty.InverseVariance'>
@pytest.mark.parametrize(
'uncertainty_type',
[StdDevUncertainty, VarianceUncertainty, InverseVariance])
def test_write_read_multiextensionfits_uncertainty_different_uncertainty_key(
tmpdir, uncertainty_type):
# Test that if a uncertainty is present it is saved and loaded by default.
ccd_data = create_ccd_data()
ccd_data.uncertainty = uncertainty_type(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename, key_uncertainty_type='Blah')
> ccd_after = CCDData.read(filename, key_uncertainty_type='Blah')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:907:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ test_write_read_multiextensionfits_not ____________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension7')
def test_write_read_multiextensionfits_not(tmpdir):
# Test that writing mask and uncertainty can be disabled
ccd_data = create_ccd_data()
ccd_data.mask = ccd_data.data > 10
ccd_data.uncertainty = StdDevUncertainty(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename, hdu_mask=None, hdu_uncertainty=None)
> ccd_after = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:921:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_____________ test_write_read_multiextensionfits_custom_ext_names ______________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_write_read_multiextension8')
def test_write_read_multiextensionfits_custom_ext_names(tmpdir):
# Test writing mask, uncertainty in another extension than default
ccd_data = create_ccd_data()
ccd_data.mask = ccd_data.data > 10
ccd_data.uncertainty = StdDevUncertainty(ccd_data.data * 10)
filename = tmpdir.join('afile.fits').strpath
ccd_data.write(filename, hdu_mask='Fun', hdu_uncertainty='NoFun')
# Try reading with defaults extension names
> ccd_after = CCDData.read(filename)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:935:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________________ test_read_old_style_multiextensionfits ____________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_read_old_style_multiexten0')
def test_read_old_style_multiextensionfits(tmpdir):
# Regression test for https://github.com/astropy/ccdproc/issues/664
#
# Prior to astropy 3.1 there was no uncertainty type saved
# in the multiextension fits files generated by CCDData
# because the uncertainty had to be StandardDevUncertainty.
#
# Current version should be able to read those in.
#
size = 4
# Value of the variables below are not important to the test.
data = np.zeros([size, size])
mask = data > 0.9
uncert = np.sqrt(data)
ccd = CCDData(data=data, mask=mask, uncertainty=uncert, unit='adu')
# We'll create the file manually to ensure we have the
# right extension names and no uncertainty type.
hdulist = ccd.to_hdu()
del hdulist[2].header['UTYPE']
file_name = tmpdir.join('old_ccddata_mef.fits').strpath
hdulist.writeto(file_name)
> ccd = CCDData.read(file_name)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
----------------------------- Captured stdout call -----------------------------
INFO: array provided for uncertainty; assuming it is a StdDevUncertainty. [astropy.nddata.ccddata]
------------------------------ Captured log call -------------------------------
INFO astropy:ccddata.py:265 array provided for uncertainty; assuming it is a StdDevUncertainty.
_________________ test_recognized_fits_formats_for_read_write __________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_recognized_fits_formats_f0')
def test_recognized_fits_formats_for_read_write(tmpdir):
# These are the extensions that are supposed to be supported.
ccd_data = create_ccd_data()
supported_extensions = ['fit', 'fits', 'fts']
for ext in supported_extensions:
path = tmpdir.join(f"test.{ext}")
ccd_data.write(path.strpath)
> from_disk = CCDData.read(path.strpath)
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________________________ test_read_returns_image ____________________________
tmpdir = local('/tmp/pytest-of-tom/pytest-1/test_read_returns_image0')
def test_read_returns_image(tmpdir):
# Test if CCData.read returns a image when reading a fits file containing
# a table and image, in that order.
tbl = Table(np.ones(10).reshape(5, 2))
img = np.ones((5, 5))
hdul = fits.HDUList(hdus=[fits.PrimaryHDU(), fits.TableHDU(tbl.as_array()),
fits.ImageHDU(img)])
filename = tmpdir.join('table_image.fits').strpath
hdul.writeto(filename)
> ccd = CCDData.read(filename, unit='adu')
pypy/site-packages/astropy/nddata/tests/test_ccddata.py:1021:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/nddata/mixins/ndio.py:56: in __call__
return registry.read(self._cls, *args, **kwargs)
pypy/site-packages/astropy/io/registry.py:523: in read
data = reader(*args, **kwargs)
pypy/site-packages/astropy/nddata/ccddata.py:665: in fits_ccddata_reader
mask=mask, uncertainty=uncertainty, wcs=wcs)
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
----------------------------- Captured stdout call -----------------------------
INFO: first HDU with data is extension 2. [astropy.nddata.ccddata]
------------------------------ Captured log call -------------------------------
INFO astropy:ccddata.py:628 first HDU with data is extension 2.
_________________________ test_pickle_uncertainty_only _________________________
def test_pickle_uncertainty_only():
ndd = NDData(np.ones(3),
uncertainty=StdDevUncertainty(np.ones(5), unit=u.m),
unit=u.m)
uncertainty_dumped = pickle.dumps(ndd.uncertainty)
uncertainty_restored = pickle.loads(uncertainty_dumped)
np.testing.assert_array_equal(ndd.uncertainty.array,
uncertainty_restored.array)
assert ndd.uncertainty.unit == uncertainty_restored.unit
# Even though it has a parent there is no one that references the parent
# after unpickling so the weakref "dies" immediately after unpickling
# finishes.
> assert uncertainty_restored.parent_nddata is None
E assert NDData([1., 1., 1.]) is None
E + where NDData([1., 1., 1.]) = StdDevUncertainty([1., 1., 1., 1., 1.]).parent_nddata
pypy/site-packages/astropy/nddata/tests/test_nddata.py:386: AssertionError
______________ TestIndex.test_index_modes[unmasked-main_col0-BST] ______________
self = <astropy.table.tests.test_index.TestIndex object at 0x000000000fdcd7f8>
main_col = [1, 2, 3, 4, 5]
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x000000000fdcd948>
engine = <class 'astropy.table.bst.BST'>
def test_index_modes(self, main_col, table_types, engine):
self._setup(main_col, table_types)
t = self.t
t.add_index('a', engine=engine)
# first, no special mode
assert len(t[[1, 3]].indices) == 1
assert len(t[::-1].indices) == 1
assert len(self._table_type(t).indices) == 1
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2 = t.copy()
# non-copy mode
with t.index_mode('discard_on_copy'):
assert len(t[[1, 3]].indices) == 0
assert len(t[::-1].indices) == 0
assert len(self._table_type(t).indices) == 0
assert len(t2.copy().indices) == 1 # mode should only affect t
# make sure non-copy mode is exited correctly
assert len(t[[1, 3]].indices) == 1
if not self.mutable:
return
# non-modify mode
with t.index_mode('freeze'):
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t['a'][0] = 6
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.add_row((2, 1.5, '12'))
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.remove_rows([1, 3])
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
assert_col_equal(t['a'], [6, 3, 5, 2])
# mode should only affect t
assert np.all(t2.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2['a'][0] = 6
assert np.all(t2.indices[0].sorted_data() == [1, 2, 3, 4, 0])
# make sure non-modify mode is exited correctly
assert np.all(t.indices[0].sorted_data() == [3, 1, 2, 0])
if isinstance(t['a'], BaseColumn):
assert len(t['a'][::-1].info.indices) == 0
with t.index_mode('copy_on_getitem'):
> assert len(t['a'][[1, 2]].info.indices) == 1
E AssertionError: assert 0 == 1
E + where 0 = len([])
E + where [] = name = a\ndtype = int64\nclass = Column\nn_bad = 0\nlength = 2\n.indices
E + where name = a\ndtype = int64\nclass = Column\nn_bad = 0\nlength = 2\n = <Column name='a' dtype='int64' length=2>\n3\n5.info
pypy/site-packages/astropy/table/tests/test_index.py:366: AssertionError
__________ TestIndex.test_index_modes[unmasked-main_col0-SortedArray] __________
self = <astropy.table.tests.test_index.TestIndex object at 0x0000000011cc10f8>
main_col = [1, 2, 3, 4, 5]
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x0000000011cc0fe0>
engine = <class 'astropy.table.sorted_array.SortedArray'>
def test_index_modes(self, main_col, table_types, engine):
self._setup(main_col, table_types)
t = self.t
t.add_index('a', engine=engine)
# first, no special mode
assert len(t[[1, 3]].indices) == 1
assert len(t[::-1].indices) == 1
assert len(self._table_type(t).indices) == 1
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2 = t.copy()
# non-copy mode
with t.index_mode('discard_on_copy'):
assert len(t[[1, 3]].indices) == 0
assert len(t[::-1].indices) == 0
assert len(self._table_type(t).indices) == 0
assert len(t2.copy().indices) == 1 # mode should only affect t
# make sure non-copy mode is exited correctly
assert len(t[[1, 3]].indices) == 1
if not self.mutable:
return
# non-modify mode
with t.index_mode('freeze'):
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t['a'][0] = 6
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.add_row((2, 1.5, '12'))
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.remove_rows([1, 3])
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
assert_col_equal(t['a'], [6, 3, 5, 2])
# mode should only affect t
assert np.all(t2.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2['a'][0] = 6
assert np.all(t2.indices[0].sorted_data() == [1, 2, 3, 4, 0])
# make sure non-modify mode is exited correctly
assert np.all(t.indices[0].sorted_data() == [3, 1, 2, 0])
if isinstance(t['a'], BaseColumn):
assert len(t['a'][::-1].info.indices) == 0
with t.index_mode('copy_on_getitem'):
> assert len(t['a'][[1, 2]].info.indices) == 1
E AssertionError: assert 0 == 1
E + where 0 = len([])
E + where [] = name = a\ndtype = int64\nclass = Column\nn_bad = 0\nlength = 2\n.indices
E + where name = a\ndtype = int64\nclass = Column\nn_bad = 0\nlength = 2\n = <Column name='a' dtype='int64' length=2>\n3\n5.info
pypy/site-packages/astropy/table/tests/test_index.py:366: AssertionError
___________ TestIndex.test_index_modes[unmasked-main_col0-SCEngine] ____________
self = <astropy.table.tests.test_index.TestIndex object at 0x0000000017a6b168>
main_col = [1, 2, 3, 4, 5]
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x0000000017a884b8>
engine = <class 'astropy.table.soco.SCEngine'>
def test_index_modes(self, main_col, table_types, engine):
self._setup(main_col, table_types)
t = self.t
t.add_index('a', engine=engine)
# first, no special mode
assert len(t[[1, 3]].indices) == 1
assert len(t[::-1].indices) == 1
assert len(self._table_type(t).indices) == 1
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2 = t.copy()
# non-copy mode
with t.index_mode('discard_on_copy'):
assert len(t[[1, 3]].indices) == 0
assert len(t[::-1].indices) == 0
assert len(self._table_type(t).indices) == 0
assert len(t2.copy().indices) == 1 # mode should only affect t
# make sure non-copy mode is exited correctly
assert len(t[[1, 3]].indices) == 1
if not self.mutable:
return
# non-modify mode
with t.index_mode('freeze'):
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t['a'][0] = 6
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.add_row((2, 1.5, '12'))
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.remove_rows([1, 3])
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
assert_col_equal(t['a'], [6, 3, 5, 2])
# mode should only affect t
assert np.all(t2.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2['a'][0] = 6
assert np.all(t2.indices[0].sorted_data() == [1, 2, 3, 4, 0])
# make sure non-modify mode is exited correctly
assert np.all(t.indices[0].sorted_data() == [3, 1, 2, 0])
if isinstance(t['a'], BaseColumn):
assert len(t['a'][::-1].info.indices) == 0
with t.index_mode('copy_on_getitem'):
> assert len(t['a'][[1, 2]].info.indices) == 1
E AssertionError: assert 0 == 1
E + where 0 = len([])
E + where [] = name = a\ndtype = int64\nclass = Column\nn_bad = 0\nlength = 2\n.indices
E + where name = a\ndtype = int64\nclass = Column\nn_bad = 0\nlength = 2\n = <Column name='a' dtype='int64' length=2>\n3\n5.info
pypy/site-packages/astropy/table/tests/test_index.py:366: AssertionError
______________ TestIndex.test_index_modes[subclass-main_col0-BST] ______________
self = <astropy.table.tests.test_index.TestIndex object at 0x000000001ffadda8>
main_col = [1, 2, 3, 4, 5]
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x000000001ffadb78>
engine = <class 'astropy.table.bst.BST'>
def test_index_modes(self, main_col, table_types, engine):
self._setup(main_col, table_types)
t = self.t
t.add_index('a', engine=engine)
# first, no special mode
assert len(t[[1, 3]].indices) == 1
assert len(t[::-1].indices) == 1
assert len(self._table_type(t).indices) == 1
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2 = t.copy()
# non-copy mode
with t.index_mode('discard_on_copy'):
assert len(t[[1, 3]].indices) == 0
assert len(t[::-1].indices) == 0
assert len(self._table_type(t).indices) == 0
assert len(t2.copy().indices) == 1 # mode should only affect t
# make sure non-copy mode is exited correctly
assert len(t[[1, 3]].indices) == 1
if not self.mutable:
return
# non-modify mode
with t.index_mode('freeze'):
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t['a'][0] = 6
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.add_row((2, 1.5, '12'))
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.remove_rows([1, 3])
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
assert_col_equal(t['a'], [6, 3, 5, 2])
# mode should only affect t
assert np.all(t2.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2['a'][0] = 6
assert np.all(t2.indices[0].sorted_data() == [1, 2, 3, 4, 0])
# make sure non-modify mode is exited correctly
assert np.all(t.indices[0].sorted_data() == [3, 1, 2, 0])
if isinstance(t['a'], BaseColumn):
assert len(t['a'][::-1].info.indices) == 0
with t.index_mode('copy_on_getitem'):
> assert len(t['a'][[1, 2]].info.indices) == 1
E AssertionError: assert 0 == 1
E + where 0 = len([])
E + where [] = name = a\ndtype = int64\nclass = MyColumn\nn_bad = 0\nlength = 2\n.indices
E + where name = a\ndtype = int64\nclass = MyColumn\nn_bad = 0\nlength = 2\n = <MyColumn name='a' dtype='int64' length=2>\n3\n5.info
pypy/site-packages/astropy/table/tests/test_index.py:366: AssertionError
__________ TestIndex.test_index_modes[subclass-main_col0-SortedArray] __________
self = <astropy.table.tests.test_index.TestIndex object at 0x00000000061302f8>
main_col = [1, 2, 3, 4, 5]
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x000000000614d980>
engine = <class 'astropy.table.sorted_array.SortedArray'>
def test_index_modes(self, main_col, table_types, engine):
self._setup(main_col, table_types)
t = self.t
t.add_index('a', engine=engine)
# first, no special mode
assert len(t[[1, 3]].indices) == 1
assert len(t[::-1].indices) == 1
assert len(self._table_type(t).indices) == 1
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2 = t.copy()
# non-copy mode
with t.index_mode('discard_on_copy'):
assert len(t[[1, 3]].indices) == 0
assert len(t[::-1].indices) == 0
assert len(self._table_type(t).indices) == 0
assert len(t2.copy().indices) == 1 # mode should only affect t
# make sure non-copy mode is exited correctly
assert len(t[[1, 3]].indices) == 1
if not self.mutable:
return
# non-modify mode
with t.index_mode('freeze'):
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t['a'][0] = 6
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.add_row((2, 1.5, '12'))
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.remove_rows([1, 3])
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
assert_col_equal(t['a'], [6, 3, 5, 2])
# mode should only affect t
assert np.all(t2.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2['a'][0] = 6
assert np.all(t2.indices[0].sorted_data() == [1, 2, 3, 4, 0])
# make sure non-modify mode is exited correctly
assert np.all(t.indices[0].sorted_data() == [3, 1, 2, 0])
if isinstance(t['a'], BaseColumn):
assert len(t['a'][::-1].info.indices) == 0
with t.index_mode('copy_on_getitem'):
> assert len(t['a'][[1, 2]].info.indices) == 1
E AssertionError: assert 0 == 1
E + where 0 = len([])
E + where [] = name = a\ndtype = int64\nclass = MyColumn\nn_bad = 0\nlength = 2\n.indices
E + where name = a\ndtype = int64\nclass = MyColumn\nn_bad = 0\nlength = 2\n = <MyColumn name='a' dtype='int64' length=2>\n3\n5.info
pypy/site-packages/astropy/table/tests/test_index.py:366: AssertionError
___________ TestIndex.test_index_modes[subclass-main_col0-SCEngine] ____________
self = <astropy.table.tests.test_index.TestIndex object at 0x000000000d5a1520>
main_col = [1, 2, 3, 4, 5]
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x000000000d5a1328>
engine = <class 'astropy.table.soco.SCEngine'>
def test_index_modes(self, main_col, table_types, engine):
self._setup(main_col, table_types)
t = self.t
t.add_index('a', engine=engine)
# first, no special mode
assert len(t[[1, 3]].indices) == 1
assert len(t[::-1].indices) == 1
assert len(self._table_type(t).indices) == 1
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2 = t.copy()
# non-copy mode
with t.index_mode('discard_on_copy'):
assert len(t[[1, 3]].indices) == 0
assert len(t[::-1].indices) == 0
assert len(self._table_type(t).indices) == 0
assert len(t2.copy().indices) == 1 # mode should only affect t
# make sure non-copy mode is exited correctly
assert len(t[[1, 3]].indices) == 1
if not self.mutable:
return
# non-modify mode
with t.index_mode('freeze'):
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t['a'][0] = 6
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.add_row((2, 1.5, '12'))
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t.remove_rows([1, 3])
assert np.all(t.indices[0].sorted_data() == [0, 1, 2, 3, 4])
assert_col_equal(t['a'], [6, 3, 5, 2])
# mode should only affect t
assert np.all(t2.indices[0].sorted_data() == [0, 1, 2, 3, 4])
t2['a'][0] = 6
assert np.all(t2.indices[0].sorted_data() == [1, 2, 3, 4, 0])
# make sure non-modify mode is exited correctly
assert np.all(t.indices[0].sorted_data() == [3, 1, 2, 0])
if isinstance(t['a'], BaseColumn):
assert len(t['a'][::-1].info.indices) == 0
with t.index_mode('copy_on_getitem'):
> assert len(t['a'][[1, 2]].info.indices) == 1
E AssertionError: assert 0 == 1
E + where 0 = len([])
E + where [] = name = a\ndtype = int64\nclass = MyColumn\nn_bad = 0\nlength = 2\n.indices
E + where name = a\ndtype = int64\nclass = MyColumn\nn_bad = 0\nlength = 2\n = <MyColumn name='a' dtype='int64' length=2>\n3\n5.info
pypy/site-packages/astropy/table/tests/test_index.py:366: AssertionError
____________________________ test_lost_parent_error ____________________________
def test_lost_parent_error():
c = table.Column([1, 2, 3], name='a')
with pytest.raises(AttributeError) as err:
> c[:].info.name
E Failed: DID NOT RAISE <class 'AttributeError'>
pypy/site-packages/astropy/table/tests/test_info.py:254: Failed
___________ TestConvertNumpyArray.test_byteswap_fits_array[unmasked] ___________
self = <astropy.table.tests.test_table.TestConvertNumpyArray object at 0x000000001173a918>
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x000000001173a800>
def test_byteswap_fits_array(self, table_types):
"""
Test for https://github.com/astropy/astropy/pull/4080, demonstrating
that FITS tables are converted to native byte order.
"""
non_native_order = ('>', '<')[sys.byteorder != 'little']
filename = get_pkg_data_filename('data/tb.fits',
'astropy.io.fits.tests')
t = table_types.Table.read(filename)
arr = t.as_array()
for idx in range(len(arr.dtype)):
assert arr.dtype[idx].byteorder != non_native_order
with fits.open(filename, character_as_bytes=True) as hdul:
data = hdul[1].data
for colname in data.columns.names:
assert np.all(data[colname] == arr[colname])
arr2 = t.as_array(keep_byteorder=True)
for colname in data.columns.names:
> assert (data[colname].dtype.byteorder ==
arr2[colname].dtype.byteorder)
pypy/site-packages/astropy/table/tests/test_table.py:1326:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ TestConvertNumpyArray.test_byteswap_fits_array[masked] ____________
self = <astropy.table.tests.test_table.TestConvertNumpyArray object at 0x0000000019f8ed40>
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x0000000019f8ec60>
def test_byteswap_fits_array(self, table_types):
"""
Test for https://github.com/astropy/astropy/pull/4080, demonstrating
that FITS tables are converted to native byte order.
"""
non_native_order = ('>', '<')[sys.byteorder != 'little']
filename = get_pkg_data_filename('data/tb.fits',
'astropy.io.fits.tests')
t = table_types.Table.read(filename)
arr = t.as_array()
for idx in range(len(arr.dtype)):
assert arr.dtype[idx].byteorder != non_native_order
with fits.open(filename, character_as_bytes=True) as hdul:
data = hdul[1].data
for colname in data.columns.names:
assert np.all(data[colname] == arr[colname])
arr2 = t.as_array(keep_byteorder=True)
for colname in data.columns.names:
> assert (data[colname].dtype.byteorder ==
arr2[colname].dtype.byteorder)
pypy/site-packages/astropy/table/tests/test_table.py:1326:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
___________ TestConvertNumpyArray.test_byteswap_fits_array[subclass] ___________
self = <astropy.table.tests.test_table.TestConvertNumpyArray object at 0x0000000021693750>
table_types = <astropy.table.tests.conftest.table_types.<locals>.TableTypes object at 0x0000000021693670>
def test_byteswap_fits_array(self, table_types):
"""
Test for https://github.com/astropy/astropy/pull/4080, demonstrating
that FITS tables are converted to native byte order.
"""
non_native_order = ('>', '<')[sys.byteorder != 'little']
filename = get_pkg_data_filename('data/tb.fits',
'astropy.io.fits.tests')
t = table_types.Table.read(filename)
arr = t.as_array()
for idx in range(len(arr.dtype)):
assert arr.dtype[idx].byteorder != non_native_order
with fits.open(filename, character_as_bytes=True) as hdul:
data = hdul[1].data
for colname in data.columns.names:
assert np.all(data[colname] == arr[colname])
arr2 = t.as_array(keep_byteorder=True)
for colname in data.columns.names:
> assert (data[colname].dtype.byteorder ==
arr2[colname].dtype.byteorder)
pypy/site-packages/astropy/table/tests/test_table.py:1326:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:381: in __exit__
self.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
____________ test_replace_update_column_via_setitem_warnings_slice _____________
def test_replace_update_column_via_setitem_warnings_slice():
"""
Test warnings related to table replace change in #5556:
Replace a slice, one warning.
"""
t = table.Table([[1, 2, 3], [4, 5, 6]], names=['a', 'b'])
with catch_warnings() as w:
with table.conf.set_temp('replace_warnings',
['refcount', 'attributes', 'slice']):
t2 = t[:2]
t2['a'] = 0 # in-place slice update
assert np.all(t['a'] == [0, 0, 3])
assert len(w) == 0
t2['a'] = [10, 20] # replace slice
> assert len(w) == 1
E assert 0 == 1
E + where 0 = len([])
pypy/site-packages/astropy/table/tests/test_table.py:2234: AssertionError
__________ test_replace_update_column_via_setitem_warnings_attributes __________
def test_replace_update_column_via_setitem_warnings_attributes():
"""
Test warnings related to table replace change in #5556:
Lost attributes.
"""
t = table.Table([[1, 2, 3], [4, 5, 6]], names=['a', 'b'])
t['a'].unit = 'm'
with catch_warnings() as w:
with table.conf.set_temp('replace_warnings',
['refcount', 'attributes', 'slice']):
t['a'] = [10, 20, 30]
> assert len(w) == 1
E assert 0 == 1
E + where 0 = len([])
pypy/site-packages/astropy/table/tests/test_table.py:2250: AssertionError
___________ test_replace_update_column_via_setitem_warnings_refcount ___________
def test_replace_update_column_via_setitem_warnings_refcount():
"""
Test warnings related to table replace change in #5556:
Reference count changes.
"""
t = table.Table([[1, 2, 3], [4, 5, 6]], names=['a', 'b'])
ta = t['a'] # Generate an extra reference to original column
with catch_warnings() as w:
with table.conf.set_temp('replace_warnings',
['refcount', 'attributes', 'slice']):
t['a'] = [10, 20, 30]
> assert len(w) == 1
E assert 0 == 1
E + where 0 = len([])
pypy/site-packages/astropy/table/tests/test_table.py:2266: AssertionError
________________________ TestTimeDelta.test_set_format _________________________
self = <astropy.time.tests.test_delta.TestTimeDelta object at 0x0000000008f6c2f8>
def test_set_format(self):
"""
Test basics of setting format attribute.
"""
dt = TimeDelta(86400.0, format='sec')
assert dt.value == 86400.0
assert dt.format == 'sec'
dt.format = 'jd'
assert dt.value == 1.0
assert dt.format == 'jd'
dt.format = 'datetime'
> assert dt.value == timedelta(days=1)
pypy/site-packages/astropy/time/tests/test_delta.py:267:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/time/core.py:1009: in value
return self.to_value(self.format, None)
pypy/site-packages/astropy/time/core.py:2402: in to_value
return super().to_value(*args, **kwargs)
pypy/site-packages/astropy/time/core.py:994: in to_value
parent=tm, **kwargs))
pypy/site-packages/astropy/time/formats.py:303: in to_value
return self.mask_if_needed(self.value)
pypy/site-packages/astropy/time/formats.py:1563: in value
microseconds=jd2_*86400*1e6)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'datetime.timedelta'>, days = 0.0, seconds = 0.0
microseconds = 0.0, milliseconds = 0, minutes = 0, hours = 0, weeks = 0
def __new__(cls, days=0, seconds=0, microseconds=0,
milliseconds=0, minutes=0, hours=0, weeks=0):
# Doing this efficiently and accurately in C is going to be difficult
# and error-prone, due to ubiquitous overflow possibilities, and that
# C double doesn't have enough bits of precision to represent
# microseconds over 10K years faithfully. The code here tries to make
# explicit where go-fast assumptions can be relied on, in order to
# guide the C implementation; it's way more convoluted than speed-
# ignoring auto-overflow-to-long idiomatic Python could be.
# XXX Check that all inputs are ints or floats.
# Final values, all integer.
# s and us fit in 32-bit signed ints; d isn't bounded.
d = s = us = 0
# Normalize everything to days, seconds, microseconds.
days += weeks*7
seconds += minutes*60 + hours*3600
microseconds += milliseconds*1000
# Get rid of all fractions, and normalize s and us.
# Take a deep breath <wink>.
if isinstance(days, float):
dayfrac, days = _math.modf(days)
daysecondsfrac, daysecondswhole = _math.modf(dayfrac * (24.*3600.))
assert daysecondswhole == int(daysecondswhole) # can't overflow
s = int(daysecondswhole)
assert days == int(days)
d = int(days)
else:
daysecondsfrac = 0.0
d = days
assert isinstance(daysecondsfrac, float)
assert abs(daysecondsfrac) <= 1.0
assert isinstance(d, int)
assert abs(s) <= 24 * 3600
# days isn't referenced again before redefinition
if isinstance(seconds, float):
secondsfrac, seconds = _math.modf(seconds)
assert seconds == int(seconds)
seconds = int(seconds)
secondsfrac += daysecondsfrac
assert abs(secondsfrac) <= 2.0
else:
secondsfrac = daysecondsfrac
# daysecondsfrac isn't referenced again
assert isinstance(secondsfrac, float)
assert abs(secondsfrac) <= 2.0
assert isinstance(seconds, int)
days, seconds = divmod(seconds, 24*3600)
d += days
s += int(seconds) # can't overflow
assert isinstance(s, int)
assert abs(s) <= 2 * 24 * 3600
# seconds isn't referenced again before redefinition
usdouble = secondsfrac * 1e6
assert abs(usdouble) < 2.1e6 # exact value not critical
# secondsfrac isn't referenced again
if isinstance(microseconds, float):
microseconds = round(microseconds + usdouble)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
else:
microseconds = int(microseconds)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
microseconds = round(microseconds + usdouble)
> assert isinstance(s, int)
E AssertionError
Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/datetime.py:434: AssertionError
_________________________ test_python_timedelta_scalar _________________________
def test_python_timedelta_scalar():
td = timedelta(days=1, seconds=1)
td1 = TimeDelta(td, format='datetime')
assert td1.sec == 86401.0
td2 = TimeDelta(86401.0, format='sec')
> assert td2.datetime == td
pypy/site-packages/astropy/time/tests/test_delta.py:575:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/time/core.py:1687: in __getattr__
return self.to_value(attr, subfmt=None)
pypy/site-packages/astropy/time/core.py:2402: in to_value
return super().to_value(*args, **kwargs)
pypy/site-packages/astropy/time/core.py:994: in to_value
parent=tm, **kwargs))
pypy/site-packages/astropy/time/formats.py:303: in to_value
return self.mask_if_needed(self.value)
pypy/site-packages/astropy/time/formats.py:1563: in value
microseconds=jd2_*86400*1e6)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'datetime.timedelta'>, days = 0.0, seconds = 1.0
microseconds = 0.0, milliseconds = 0, minutes = 0, hours = 0, weeks = 0
def __new__(cls, days=0, seconds=0, microseconds=0,
milliseconds=0, minutes=0, hours=0, weeks=0):
# Doing this efficiently and accurately in C is going to be difficult
# and error-prone, due to ubiquitous overflow possibilities, and that
# C double doesn't have enough bits of precision to represent
# microseconds over 10K years faithfully. The code here tries to make
# explicit where go-fast assumptions can be relied on, in order to
# guide the C implementation; it's way more convoluted than speed-
# ignoring auto-overflow-to-long idiomatic Python could be.
# XXX Check that all inputs are ints or floats.
# Final values, all integer.
# s and us fit in 32-bit signed ints; d isn't bounded.
d = s = us = 0
# Normalize everything to days, seconds, microseconds.
days += weeks*7
seconds += minutes*60 + hours*3600
microseconds += milliseconds*1000
# Get rid of all fractions, and normalize s and us.
# Take a deep breath <wink>.
if isinstance(days, float):
dayfrac, days = _math.modf(days)
daysecondsfrac, daysecondswhole = _math.modf(dayfrac * (24.*3600.))
assert daysecondswhole == int(daysecondswhole) # can't overflow
s = int(daysecondswhole)
assert days == int(days)
d = int(days)
else:
daysecondsfrac = 0.0
d = days
assert isinstance(daysecondsfrac, float)
assert abs(daysecondsfrac) <= 1.0
assert isinstance(d, int)
assert abs(s) <= 24 * 3600
# days isn't referenced again before redefinition
if isinstance(seconds, float):
secondsfrac, seconds = _math.modf(seconds)
assert seconds == int(seconds)
seconds = int(seconds)
secondsfrac += daysecondsfrac
assert abs(secondsfrac) <= 2.0
else:
secondsfrac = daysecondsfrac
# daysecondsfrac isn't referenced again
assert isinstance(secondsfrac, float)
assert abs(secondsfrac) <= 2.0
assert isinstance(seconds, int)
days, seconds = divmod(seconds, 24*3600)
d += days
s += int(seconds) # can't overflow
assert isinstance(s, int)
assert abs(s) <= 2 * 24 * 3600
# seconds isn't referenced again before redefinition
usdouble = secondsfrac * 1e6
assert abs(usdouble) < 2.1e6 # exact value not critical
# secondsfrac isn't referenced again
if isinstance(microseconds, float):
microseconds = round(microseconds + usdouble)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
else:
microseconds = int(microseconds)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
microseconds = round(microseconds + usdouble)
> assert isinstance(s, int)
E AssertionError
Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/datetime.py:434: AssertionError
_________________________ test_python_timedelta_vector _________________________
def test_python_timedelta_vector():
td = [[timedelta(days=1), timedelta(days=2)],
[timedelta(days=3), timedelta(days=4)]]
td1 = TimeDelta(td, format='datetime')
assert np.all(td1.jd == [[1, 2], [3, 4]])
td2 = TimeDelta([[1, 2], [3, 4]], format='jd')
> assert np.all(td2.datetime == td)
pypy/site-packages/astropy/time/tests/test_delta.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/time/core.py:1687: in __getattr__
return self.to_value(attr, subfmt=None)
pypy/site-packages/astropy/time/core.py:2402: in to_value
return super().to_value(*args, **kwargs)
pypy/site-packages/astropy/time/core.py:994: in to_value
parent=tm, **kwargs))
pypy/site-packages/astropy/time/formats.py:303: in to_value
return self.mask_if_needed(self.value)
pypy/site-packages/astropy/time/formats.py:1563: in value
microseconds=jd2_*86400*1e6)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'datetime.timedelta'>, days = 0.0, seconds = 0.0
microseconds = 0.0, milliseconds = 0, minutes = 0, hours = 0, weeks = 0
def __new__(cls, days=0, seconds=0, microseconds=0,
milliseconds=0, minutes=0, hours=0, weeks=0):
# Doing this efficiently and accurately in C is going to be difficult
# and error-prone, due to ubiquitous overflow possibilities, and that
# C double doesn't have enough bits of precision to represent
# microseconds over 10K years faithfully. The code here tries to make
# explicit where go-fast assumptions can be relied on, in order to
# guide the C implementation; it's way more convoluted than speed-
# ignoring auto-overflow-to-long idiomatic Python could be.
# XXX Check that all inputs are ints or floats.
# Final values, all integer.
# s and us fit in 32-bit signed ints; d isn't bounded.
d = s = us = 0
# Normalize everything to days, seconds, microseconds.
days += weeks*7
seconds += minutes*60 + hours*3600
microseconds += milliseconds*1000
# Get rid of all fractions, and normalize s and us.
# Take a deep breath <wink>.
if isinstance(days, float):
dayfrac, days = _math.modf(days)
daysecondsfrac, daysecondswhole = _math.modf(dayfrac * (24.*3600.))
assert daysecondswhole == int(daysecondswhole) # can't overflow
s = int(daysecondswhole)
assert days == int(days)
d = int(days)
else:
daysecondsfrac = 0.0
d = days
assert isinstance(daysecondsfrac, float)
assert abs(daysecondsfrac) <= 1.0
assert isinstance(d, int)
assert abs(s) <= 24 * 3600
# days isn't referenced again before redefinition
if isinstance(seconds, float):
secondsfrac, seconds = _math.modf(seconds)
assert seconds == int(seconds)
seconds = int(seconds)
secondsfrac += daysecondsfrac
assert abs(secondsfrac) <= 2.0
else:
secondsfrac = daysecondsfrac
# daysecondsfrac isn't referenced again
assert isinstance(secondsfrac, float)
assert abs(secondsfrac) <= 2.0
assert isinstance(seconds, int)
days, seconds = divmod(seconds, 24*3600)
d += days
s += int(seconds) # can't overflow
assert isinstance(s, int)
assert abs(s) <= 2 * 24 * 3600
# seconds isn't referenced again before redefinition
usdouble = secondsfrac * 1e6
assert abs(usdouble) < 2.1e6 # exact value not critical
# secondsfrac isn't referenced again
if isinstance(microseconds, float):
microseconds = round(microseconds + usdouble)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
else:
microseconds = int(microseconds)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
microseconds = round(microseconds + usdouble)
> assert isinstance(s, int)
E AssertionError
Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/datetime.py:434: AssertionError
__________________________ test_timedelta_to_datetime __________________________
def test_timedelta_to_datetime():
td = TimeDelta(1, format='jd')
> assert td.to_datetime() == timedelta(days=1)
pypy/site-packages/astropy/time/tests/test_delta.py:593:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/time/core.py:2124: in to_datetime
return tm._shaped_like_input(tm._time.value)
pypy/site-packages/astropy/time/formats.py:1563: in value
microseconds=jd2_*86400*1e6)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'datetime.timedelta'>, days = 0.0, seconds = 0.0
microseconds = 0.0, milliseconds = 0, minutes = 0, hours = 0, weeks = 0
def __new__(cls, days=0, seconds=0, microseconds=0,
milliseconds=0, minutes=0, hours=0, weeks=0):
# Doing this efficiently and accurately in C is going to be difficult
# and error-prone, due to ubiquitous overflow possibilities, and that
# C double doesn't have enough bits of precision to represent
# microseconds over 10K years faithfully. The code here tries to make
# explicit where go-fast assumptions can be relied on, in order to
# guide the C implementation; it's way more convoluted than speed-
# ignoring auto-overflow-to-long idiomatic Python could be.
# XXX Check that all inputs are ints or floats.
# Final values, all integer.
# s and us fit in 32-bit signed ints; d isn't bounded.
d = s = us = 0
# Normalize everything to days, seconds, microseconds.
days += weeks*7
seconds += minutes*60 + hours*3600
microseconds += milliseconds*1000
# Get rid of all fractions, and normalize s and us.
# Take a deep breath <wink>.
if isinstance(days, float):
dayfrac, days = _math.modf(days)
daysecondsfrac, daysecondswhole = _math.modf(dayfrac * (24.*3600.))
assert daysecondswhole == int(daysecondswhole) # can't overflow
s = int(daysecondswhole)
assert days == int(days)
d = int(days)
else:
daysecondsfrac = 0.0
d = days
assert isinstance(daysecondsfrac, float)
assert abs(daysecondsfrac) <= 1.0
assert isinstance(d, int)
assert abs(s) <= 24 * 3600
# days isn't referenced again before redefinition
if isinstance(seconds, float):
secondsfrac, seconds = _math.modf(seconds)
assert seconds == int(seconds)
seconds = int(seconds)
secondsfrac += daysecondsfrac
assert abs(secondsfrac) <= 2.0
else:
secondsfrac = daysecondsfrac
# daysecondsfrac isn't referenced again
assert isinstance(secondsfrac, float)
assert abs(secondsfrac) <= 2.0
assert isinstance(seconds, int)
days, seconds = divmod(seconds, 24*3600)
d += days
s += int(seconds) # can't overflow
assert isinstance(s, int)
assert abs(s) <= 2 * 24 * 3600
# seconds isn't referenced again before redefinition
usdouble = secondsfrac * 1e6
assert abs(usdouble) < 2.1e6 # exact value not critical
# secondsfrac isn't referenced again
if isinstance(microseconds, float):
microseconds = round(microseconds + usdouble)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
else:
microseconds = int(microseconds)
seconds, microseconds = divmod(microseconds, 1000000)
days, seconds = divmod(seconds, 24*3600)
d += days
s += seconds
microseconds = round(microseconds + usdouble)
> assert isinstance(s, int)
E AssertionError
Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/datetime.py:434: AssertionError
__________________________________ test_slice __________________________________
def test_slice():
mywcs = WCS(naxis=2)
mywcs.wcs.crval = [1, 1]
mywcs.wcs.cdelt = [0.1, 0.1]
mywcs.wcs.crpix = [1, 1]
mywcs._naxis = [1000, 500]
pscale = 0.1 # from cdelt
slice_wcs = mywcs.slice([slice(1, None), slice(0, None)])
assert np.all(slice_wcs.wcs.crpix == np.array([1, 0]))
assert slice_wcs._naxis == [1000, 499]
# test that CRPIX maps to CRVAL:
assert_allclose(
slice_wcs.wcs_pix2world(*slice_wcs.wcs.crpix, 1),
slice_wcs.wcs.crval, rtol=0.0, atol=1e-6 * pscale
)
slice_wcs = mywcs.slice([slice(1, None, 2), slice(0, None, 4)])
assert np.all(slice_wcs.wcs.crpix == np.array([0.625, 0.25]))
assert np.all(slice_wcs.wcs.cdelt == np.array([0.4, 0.2]))
assert slice_wcs._naxis == [250, 250]
slice_wcs = mywcs.slice([slice(None, None, 2), slice(0, None, 2)])
assert np.all(slice_wcs.wcs.cdelt == np.array([0.2, 0.2]))
assert slice_wcs._naxis == [500, 250]
# Non-integral values do not alter the naxis attribute
with pytest.warns(AstropyUserWarning):
> slice_wcs = mywcs.slice([slice(50.), slice(20.)])
pypy/site-packages/astropy/wcs/tests/test_utils.py:139:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WCS Keywords
Number of WCS axes: 2
CTYPE : '' ''
CRVAL : 1.0 1.0
CRPIX : 1.0 1.0
PC1_1 PC1_2 : 1.0 0.0
PC2_1 PC2_2 : 0.0 1.0
CDELT : 0.1 0.1
NAXIS : 1000 500
view = [slice(None, 50.0, None), slice(None, 20.0, None)], numpy_order = True
def slice(self, view, numpy_order=True):
"""
Slice a WCS instance using a Numpy slice. The order of the slice should
be reversed (as for the data) compared to the natural WCS order.
Parameters
----------
view : tuple
A tuple containing the same number of slices as the WCS system.
The ``step`` method, the third argument to a slice, is not
presently supported.
numpy_order : bool
Use numpy order, i.e. slice the WCS so that an identical slice
applied to a numpy array will slice the array and WCS in the same
way. If set to `False`, the WCS will be sliced in FITS order,
meaning the first slice will be applied to the *last* numpy index
but the *first* WCS axis.
Returns
-------
wcs_new : `~astropy.wcs.WCS`
A new resampled WCS axis
"""
if hasattr(view, '__len__') and len(view) > self.wcs.naxis:
raise ValueError("Must have # of slices <= # of WCS axes")
elif not hasattr(view, '__len__'): # view MUST be an iterable
view = [view]
if not all(isinstance(x, slice) for x in view):
# We need to drop some dimensions, but this may not always be
# possible with .sub due to correlated axes, so instead we use the
# generalized slicing infrastructure from astropy.wcs.wcsapi.
return SlicedFITSWCS(self, view)
# NOTE: we could in principle use SlicedFITSWCS as above for all slicing,
# but in the simple case where there are no axes dropped, we can just
# create a full WCS object with updated WCS parameters which is faster
# for this specific case and also backward-compatible.
wcs_new = self.deepcopy()
if wcs_new.sip is not None:
sip_crpix = wcs_new.sip.crpix.tolist()
for i, iview in enumerate(view):
if iview.step is not None and iview.step < 0:
raise NotImplementedError("Reversing an axis is not "
"implemented.")
if numpy_order:
wcs_index = self.wcs.naxis - 1 - i
else:
wcs_index = i
if iview.step is not None and iview.start is None:
# Slice from "None" is equivalent to slice from 0 (but one
# might want to downsample, so allow slices with
# None,None,step or None,stop,step)
iview = slice(0, iview.stop, iview.step)
if iview.start is not None:
if iview.step not in (None, 1):
crpix = self.wcs.crpix[wcs_index]
cdelt = self.wcs.cdelt[wcs_index]
# equivalently (keep this comment so you can compare eqns):
# wcs_new.wcs.crpix[wcs_index] =
# (crpix - iview.start)*iview.step + 0.5 - iview.step/2.
crp = ((crpix - iview.start - 1.)/iview.step
+ 0.5 + 1./iview.step/2.)
wcs_new.wcs.crpix[wcs_index] = crp
if wcs_new.sip is not None:
sip_crpix[wcs_index] = crp
wcs_new.wcs.cdelt[wcs_index] = cdelt * iview.step
else:
wcs_new.wcs.crpix[wcs_index] -= iview.start
if wcs_new.sip is not None:
sip_crpix[wcs_index] -= iview.start
try:
# range requires integers but the other attributes can also
# handle arbitrary values, so this needs to be in a try/except.
> nitems = len(builtins.range(self._naxis[wcs_index])[iview])
E TypeError: 'float' object cannot be interpreted as an integer
pypy/site-packages/astropy/wcs/wcs.py:2997: TypeError
__________________________ test_validate_with_2_wcses __________________________
def test_validate_with_2_wcses():
# From Issue #2053
with pytest.warns(AstropyUserWarning):
> results = wcs.validate(get_pkg_data_filename("data/2wcses.hdr"))
pypy/site-packages/astropy/wcs/tests/test_wcs.py:423:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
source = '/home/tom/pypy/site-packages/astropy/wcs/tests/data/2wcses.hdr'
def validate(source):
"""
Prints a WCS validation report for the given FITS file.
Parameters
----------
source : str path, readable file-like object or `astropy.io.fits.HDUList` object
The FITS file to validate.
Returns
-------
results : WcsValidateResults instance
The result is returned as nested lists. The first level
corresponds to the HDUs in the given file. The next level has
an entry for each WCS found in that header. The special
subclass of list will pretty-print the results as a table when
printed.
"""
class _WcsValidateWcsResult(list):
def __init__(self, key):
self._key = key
def __repr__(self):
result = [" WCS key '{}':".format(self._key or ' ')]
if len(self):
for entry in self:
for i, line in enumerate(entry.splitlines()):
if i == 0:
initial_indent = ' - '
else:
initial_indent = ' '
result.extend(
textwrap.wrap(
line,
initial_indent=initial_indent,
subsequent_indent=' '))
else:
result.append(" No issues.")
return '\n'.join(result)
class _WcsValidateHduResult(list):
def __init__(self, hdu_index, hdu_name):
self._hdu_index = hdu_index
self._hdu_name = hdu_name
list.__init__(self)
def __repr__(self):
if len(self):
if self._hdu_name:
hdu_name = f' ({self._hdu_name})'
else:
hdu_name = ''
result = [f'HDU {self._hdu_index}{hdu_name}:']
for wcs in self:
result.append(repr(wcs))
return '\n'.join(result)
return ''
class _WcsValidateResults(list):
def __repr__(self):
result = []
for hdu in self:
content = repr(hdu)
if len(content):
result.append(content)
return '\n\n'.join(result)
global __warningregistry__
if isinstance(source, fits.HDUList):
hdulist = source
else:
hdulist = fits.open(source)
results = _WcsValidateResults()
for i, hdu in enumerate(hdulist):
hdu_results = _WcsValidateHduResult(i, hdu.name)
results.append(hdu_results)
with warnings.catch_warnings(record=True) as warning_lines:
wcses = find_all_wcs(
hdu.header, relax=_wcs.WCSHDR_reject,
fix=False, _do_set=False)
for wcs in wcses:
wcs_results = _WcsValidateWcsResult(wcs.wcs.alt)
hdu_results.append(wcs_results)
try:
> del __warningregistry__
E KeyError: '__warningregistry__'
pypy/site-packages/astropy/wcs/wcs.py:3311: KeyError
___________________________ test_validate_faulty_wcs ___________________________
@pytest.mark.filterwarnings('ignore')
def test_validate_faulty_wcs():
"""
From github issue #2053
"""
h = fits.Header()
# Illegal WCS:
h['RADESYSA'] = 'ICRS'
h['PV2_1'] = 1.0
hdu = fits.PrimaryHDU([[0]], header=h)
hdulist = fits.HDUList([hdu])
# Check that this doesn't raise a NameError exception
> wcs.validate(hdulist)
pypy/site-packages/astropy/wcs/tests/test_wcs.py:663:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
source = [<astropy.io.fits.hdu.image.PrimaryHDU object at 0x000000000ee29e88>]
def validate(source):
"""
Prints a WCS validation report for the given FITS file.
Parameters
----------
source : str path, readable file-like object or `astropy.io.fits.HDUList` object
The FITS file to validate.
Returns
-------
results : WcsValidateResults instance
The result is returned as nested lists. The first level
corresponds to the HDUs in the given file. The next level has
an entry for each WCS found in that header. The special
subclass of list will pretty-print the results as a table when
printed.
"""
class _WcsValidateWcsResult(list):
def __init__(self, key):
self._key = key
def __repr__(self):
result = [" WCS key '{}':".format(self._key or ' ')]
if len(self):
for entry in self:
for i, line in enumerate(entry.splitlines()):
if i == 0:
initial_indent = ' - '
else:
initial_indent = ' '
result.extend(
textwrap.wrap(
line,
initial_indent=initial_indent,
subsequent_indent=' '))
else:
result.append(" No issues.")
return '\n'.join(result)
class _WcsValidateHduResult(list):
def __init__(self, hdu_index, hdu_name):
self._hdu_index = hdu_index
self._hdu_name = hdu_name
list.__init__(self)
def __repr__(self):
if len(self):
if self._hdu_name:
hdu_name = f' ({self._hdu_name})'
else:
hdu_name = ''
result = [f'HDU {self._hdu_index}{hdu_name}:']
for wcs in self:
result.append(repr(wcs))
return '\n'.join(result)
return ''
class _WcsValidateResults(list):
def __repr__(self):
result = []
for hdu in self:
content = repr(hdu)
if len(content):
result.append(content)
return '\n\n'.join(result)
global __warningregistry__
if isinstance(source, fits.HDUList):
hdulist = source
else:
hdulist = fits.open(source)
results = _WcsValidateResults()
for i, hdu in enumerate(hdulist):
hdu_results = _WcsValidateHduResult(i, hdu.name)
results.append(hdu_results)
with warnings.catch_warnings(record=True) as warning_lines:
wcses = find_all_wcs(
hdu.header, relax=_wcs.WCSHDR_reject,
fix=False, _do_set=False)
for wcs in wcses:
wcs_results = _WcsValidateWcsResult(wcs.wcs.alt)
hdu_results.append(wcs_results)
try:
> del __warningregistry__
E KeyError: '__warningregistry__'
pypy/site-packages/astropy/wcs/wcs.py:3311: KeyError
________________________________ test_to_fits_1 ________________________________
def test_to_fits_1():
"""
Test to_fits() with LookupTable distortion.
"""
fits_name = get_pkg_data_filename('data/dist.fits')
with pytest.warns(AstropyDeprecationWarning):
> w = wcs.WCS(fits_name)
pypy/site-packages/astropy/wcs/tests/test_wcs.py:1126:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pypy/site-packages/astropy/wcs/wcs.py:510: in __init__
fd.close()
pypy/site-packages/astropy/io/fits/hdu/hdulist.py:966: in close
self._file.close()
pypy/site-packages/astropy/io/fits/file.py:413: in close
self._maybe_close_mmap()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <astropy.io.fits.file._File <_io.FileIO [closed]>>, refcount_delta = 0
def _maybe_close_mmap(self, refcount_delta=0):
"""
When mmap is in use these objects hold a reference to the mmap of the
file (so there is only one, shared by all HDUs that reference this
file).
This will close the mmap if there are no arrays referencing it.
"""
if (self._mmap is not None and
> sys.getrefcount(self._mmap) == 2 + refcount_delta):
E AttributeError: module 'sys' has no attribute 'getrefcount'
pypy/site-packages/astropy/io/fits/file.py:431: AttributeError
_________________________________ test_compare _________________________________
def test_compare():
header = get_pkg_data_contents('data/3d_cd.hdr', encoding='binary')
w = _wcs.Wcsprm(header)
w2 = _wcs.Wcsprm(header)
assert w == w2
w.equinox = 42
assert w == w2
assert not w.compare(w2)
assert w.compare(w2, _wcs.WCSCOMPARE_ANCILLARY)
w = _wcs.Wcsprm(header)
w2 = _wcs.Wcsprm(header)
with pytest.warns(RuntimeWarning):
w.cdelt[0] = np.float32(0.00416666666666666666666666)
w2.cdelt[0] = np.float64(0.00416666666666666666666666)
assert not w.compare(w2)
> assert w.compare(w2, tolerance=1e-6)
E Failed: DID NOT WARN. No warnings of type (<class 'RuntimeWarning'>,) was emitted. The list of emitted warnings is: [UserWarning('cdelt will be ignored since cd is present',), UserWarning('cdelt will be ignored since cd is present',)].
pypy/site-packages/astropy/wcs/tests/test_wcsprm.py:921: Failed
=============================== warnings summary ===============================
pypy/site-packages/astropy/io/ascii/tests/test_read.py::test_read_chunks_formats[False]
/home/tom/pypy/site-packages/astropy/table/table.py:1188: ResourceWarning: unclosed file <_io.BufferedReader name='data/ipac.dat.bz2'>
for col in cols:
pypy/site-packages/astropy/io/ascii/tests/test_read.py::test_read_chunks_formats[False]
/home/tom/pypy/site-packages/astropy/table/table.py:1188: ResourceWarning: unclosed file <_io.TextIOWrapper name='data/test5.dat' mode='r' encoding='UTF-8'>
for col in cols:
pypy/site-packages/astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_scaled_data
/home/tom/pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1186: VerifyWarning: Error validating header for HDU #1 (note: Astropy uses zero-based indexing).
I/O operation on closed file
There may be extra bytes after the last HDU or the file is corrupted.
len(self), indent(str(exc))), VerifyWarning)
pypy/site-packages/astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_uint16_data
/home/tom/pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1186: VerifyWarning: Error validating header for HDU #7 (note: Astropy uses zero-based indexing).
I/O operation on closed file
There may be extra bytes after the last HDU or the file is corrupted.
len(self), indent(str(exc))), VerifyWarning)
pypy/site-packages/astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_compressed_image_data
pypy/site-packages/astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_compressed_image_data_int16
pypy/site-packages/astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_compressed_image_data_float32
pypy/site-packages/astropy/io/fits/tests/test_core.py::TestCore::test_uint
/home/tom/pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1186: VerifyWarning: Error validating header for HDU #2 (note: Astropy uses zero-based indexing).
I/O operation on closed file
There may be extra bytes after the last HDU or the file is corrupted.
len(self), indent(str(exc))), VerifyWarning)
pypy/site-packages/astropy/io/fits/tests/test_core.py::TestCore::test_consecutive_writeto
/home/tom/pypy/site-packages/astropy/io/fits/card.py:1151: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/blank.fits' mode='rb' closefd=True>
m = self._value_NFSC_RE.match(valuecomment)
pypy/site-packages/astropy/io/fits/tests/test_core.py::TestCore::test_consecutive_writeto
/home/tom/pypy/site-packages/astropy/io/fits/card.py:1151: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/tb.fits' mode='rb' closefd=True>
m = self._value_NFSC_RE.match(valuecomment)
pypy/site-packages/astropy/io/fits/tests/test_core.py::TestCore::test_consecutive_writeto
/home/tom/pypy/site-packages/astropy/io/fits/hdu/hdulist.py:1186: VerifyWarning: Error validating header for HDU #5 (note: Astropy uses zero-based indexing).
I/O operation on closed file
There may be extra bytes after the last HDU or the file is corrupted.
len(self), indent(str(exc))), VerifyWarning)
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-9ktq56fk/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/arange.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-gma8_hrz/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-bc5wj_o1/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-ffvw5e7v/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-73vyvwyr/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-5384opjo/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-qrlv8i5n/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-4df0_3ee/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-vg1rz51x/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-ojbin04c/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_fitstime.py::TestFitsTime::test_fits_to_time_meta[QTable]
/home/tom/pypy/site-packages/astropy/io/fits/card.py:775: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-h3v6bwad/testb.fits' mode='rb' closefd=True>
numr = self._number_NFSC_RE.match(m.group('numr'))
pypy/site-packages/astropy/io/fits/tests/test_hdulist.py::TestHDUListFunctions::test_open_file_with_end_padding
/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/ast.py:187: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/test0.fits' mode='rb' closefd=True>
for item in field:
pypy/site-packages/astropy/io/fits/tests/test_image.py::TestImageFunctions::test_fortran_array_non_contiguous
/home/tom/pypy/site-packages/_pytest/_code/source.py:294: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-87wlnx15/test.fits' mode='rb' closefd=True>
for x in ast.walk(node):
pypy/site-packages/astropy/io/fits/tests/test_table.py::TestTableFunctions::test_numpy_ndarray_to_bintablehdu
/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/ast.py:183: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-2bfxsyk5/tmp.fits' mode='rb' closefd=True>
for name, field in iter_fields(node):
pypy/site-packages/astropy/io/fits/tests/test_table.py::TestTableFunctions::test_numpy_ndarray_to_bintablehdu
/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/ast.py:183: ResourceWarning: unclosed file <_io.FileIO name='/tmp/fits-test-6hwrf8xy/tmp.fits' mode='rb' closefd=True>
for name, field in iter_fields(node):
pypy/site-packages/astropy/io/fits/tests/test_table.py::TestTableFunctions::test_numpy_ndarray_to_bintablehdu
/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/ast.py:183: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/tb.fits' mode='rb' closefd=True>
for name, field in iter_fields(node):
pypy/site-packages/astropy/io/fits/tests/test_table.py::TestTableFunctions::test_numpy_ndarray_to_bintablehdu
/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/ast.py:183: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/test0.fits' mode='rb' closefd=True>
for name, field in iter_fields(node):
pypy/site-packages/astropy/io/fits/tests/test_table.py::TestTableFunctions::test_numpy_ndarray_to_bintablehdu
/home/tom/Downloads/pypy3.6-7.2.0-linux_x86_64-portable/lib-python/3/ast.py:183: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/io/fits/tests/data/ascii.fits' mode='rb' closefd=True>
for name, field in iter_fields(node):
pypy/site-packages/astropy/stats/tests/test_biweight.py::test_biweight_location_masked
/home/tom/pypy/site-packages/numpy/ma/core.py:4596: ResourceWarning: unclosed <socket.socket fd=10, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=0, laddr=('127.0.0.1', 40747)>
result = self._data.reshape(*s, **kwargs).view(type(self))
pypy/site-packages/astropy/wcs/tests/test_utils.py::test_noncelestial_scale[cdelt0-pc0-cd0]
pypy/site-packages/astropy/wcs/tests/test_utils.py::test_noncelestial_scale[cdelt1-pc1-cd1]
pypy/site-packages/astropy/wcs/tests/test_utils.py::test_noncelestial_scale[cdelt3-None-cd3]
/home/tom/pypy/site-packages/astropy/wcs/tests/test_utils.py:594: UserWarning: cdelt will be ignored since cd is present
mywcs.wcs.cdelt = cdelt
pypy/site-packages/astropy/wcs/tests/test_utils.py::test_noncelestial_scale[cdelt0-pc0-cd0]
pypy/site-packages/astropy/wcs/tests/test_utils.py::test_noncelestial_scale[cdelt1-pc1-cd1]
pypy/site-packages/astropy/wcs/tests/test_utils.py::test_noncelestial_scale[cdelt3-None-cd3]
/home/tom/pypy/site-packages/astropy/wcs/wcs.py:3081: UserWarning: cdelt will be ignored since cd is present
cdelt = np.dot(self.wcs.cd, np.diag(self.wcs.cdelt))
pypy/site-packages/astropy/wcs/tests/test_wcsprm.py::test_sub_segfault
/home/tom/pypy/lib-python/3/importlib/_bootstrap.py:177: ResourceWarning: unclosed file <_io.FileIO name='/home/tom/pypy/site-packages/astropy/wcs/tests/data/validate.fits' mode='rb' closefd=True>
_imp.acquire_lock()
-- Docs: https://docs.pytest.org/en/latest/warnings.html
= 274 failed, 12242 passed, 1072 skipped, 52 xfailed, 38 warnings in 270.15s (0:04:30) =
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