def test_wcs_keyword_removal_for_wcs_test_files():
"""
Test, for the WCS test files, that keyword removall works as
expected. Those cover a much broader range of WCS types than
test_wcs_keywords_removed_from_header
"""
from astropy.nddata.ccddata import _generate_wcs_and_update_header
from astropy.nddata.ccddata import _KEEP_THESE_KEYWORDS_IN_HEADER
keepers = set(_KEEP_THESE_KEYWORDS_IN_HEADER)
wcs_headers = get_pkg_data_filenames('../../wcs/tests/data',
pattern='*.hdr')
for hdr in wcs_headers:
# Skip the files that are expected to be bad...
if 'invalid' in hdr or 'nonstandard' in hdr or 'segfault' in hdr:
continue
header_string = get_pkg_data_contents(hdr)
wcs = WCS(header_string)
header = wcs.to_header(relax=True)
new_header, new_wcs = _generate_wcs_and_update_header(header)
# Make sure all of the WCS-related keywords have been removed.
assert not (set(new_header) &
set(new_wcs.to_header(relax=True)) -
keepers)
# Check that the new wcs is the same as the old.
new_wcs_header = new_wcs.to_header(relax=True)
for k, v in new_wcs_header.items():
if isinstance(v, str):
assert header[k] == v
else:
np.testing.assert_almost_equal(header[k], v)
def test_wcs_keyword_removal_for_wcs_test_files():
"""
Test, for the WCS test files, that keyword removall works as
expected. Those cover a much broader range of WCS types than
test_wcs_keywords_removed_from_header
"""
from astropy.nddata.ccddata import _generate_wcs_and_update_header
from astropy.nddata.ccddata import _KEEP_THESE_KEYWORDS_IN_HEADER
keepers = set(_KEEP_THESE_KEYWORDS_IN_HEADER)
wcs_headers = get_pkg_data_filenames('../../wcs/tests/data',
pattern='*.hdr')
for hdr in wcs_headers:
# Skip the files that are expected to be bad...
if 'invalid' in hdr or 'nonstandard' in hdr or 'segfault' in hdr:
continue
header_string = get_pkg_data_contents(hdr)
wcs = WCS(header_string)
header = wcs.to_header(relax=True)
new_header, new_wcs = _generate_wcs_and_update_header(header)
# Make sure all of the WCS-related keywords have been removed.
assert not (set(new_header)
& set(new_wcs.to_header(relax=True)) - keepers)
# Check that the new wcs is the same as the old.
new_wcs_header = new_wcs.to_header(relax=True)
for k, v in new_wcs_header.items():
if isinstance(v, str):
assert header[k] == v
else:
np.testing.assert_almost_equal(header[k], v)
def test_wcs_keyword_removal_for_wcs_test_files():
"""
Test, for the WCS test files, that keyword removal works as
expected. Those cover a much broader range of WCS types than
test_wcs_keywords_removed_from_header.
Includes regression test for #8597
"""
from astropy.nddata.ccddata import _generate_wcs_and_update_header
from astropy.nddata.ccddata import (_KEEP_THESE_KEYWORDS_IN_HEADER,
_CDs, _PCs)
keepers = set(_KEEP_THESE_KEYWORDS_IN_HEADER)
wcs_headers = get_pkg_data_filenames('../../wcs/tests/data',
pattern='*.hdr')
for hdr in wcs_headers:
# Skip the files that are expected to be bad...
if ('invalid' in hdr or 'nonstandard' in hdr or 'segfault' in hdr or
'chandra-pixlist-wcs' in hdr):
continue
header_string = get_pkg_data_contents(hdr)
header = fits.Header.fromstring(header_string)
wcs = WCS(header_string)
header_from_wcs = wcs.to_header(relax=True)
new_header, new_wcs = _generate_wcs_and_update_header(header)
new_wcs_header = new_wcs.to_header(relax=True)
# Make sure all of the WCS-related keywords generated by astropy
# have been removed.
assert not (set(new_header) &
set(new_wcs_header) -
keepers)
# Check that new_header contains no remaining WCS information.
# Specifically, check that
# 1. The combination of new_header and new_wcs does not contain
# both PCi_j and CDi_j keywords. See #8597.
# Check for 1
final_header = new_header + new_wcs_header
final_header_set = set(final_header)
if _PCs & final_header_set:
assert not (_CDs & final_header_set)
elif _CDs & final_header_set:
assert not (_PCs & final_header_set)
# Check that the new wcs is the same as the old.
for k, v in new_wcs_header.items():
if isinstance(v, str):
assert header_from_wcs[k] == v
else:
np.testing.assert_almost_equal(header_from_wcs[k], v)
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 get_pkg_data_filenames('data', pattern='*.fits'):
if sys.platform == 'win32' and filename.endswith('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', 'theap-gap.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)
# Test that creating an HDUList from something silly raises a TypeError
pytest.raises(TypeError, fits.HDUList.fromstring, ['a', 'b', 'c'])
def test_wcs_keyword_removal_for_wcs_test_files():
"""
Test, for the WCS test files, that keyword removal works as
expected. Those cover a much broader range of WCS types than
test_wcs_keywords_removed_from_header.
Includes regression test for #8597
"""
from astropy.nddata.ccddata import _generate_wcs_and_update_header
from astropy.nddata.ccddata import (_KEEP_THESE_KEYWORDS_IN_HEADER,
_CDs, _PCs)
keepers = set(_KEEP_THESE_KEYWORDS_IN_HEADER)
wcs_headers = get_pkg_data_filenames('../../wcs/tests/data',
pattern='*.hdr')
for hdr in wcs_headers:
# Skip the files that are expected to be bad...
if 'invalid' in hdr or 'nonstandard' in hdr or 'segfault' in hdr:
continue
header_string = get_pkg_data_contents(hdr)
header = fits.Header.fromstring(header_string)
wcs = WCS(header_string)
header_from_wcs = wcs.to_header(relax=True)
new_header, new_wcs = _generate_wcs_and_update_header(header)
new_wcs_header = new_wcs.to_header(relax=True)
# Make sure all of the WCS-related keywords generated by astropy
# have been removed.
assert not (set(new_header) &
set(new_wcs_header) -
keepers)
# Check that new_header contains no remaining WCS information.
# Specifically, check that
# 1. The combination of new_header and new_wcs does not contain
# both PCi_j and CDi_j keywords. See #8597.
# Check for 1
final_header = new_header + new_wcs_header
final_header_set = set(final_header)
if _PCs & final_header_set:
assert not (_CDs & final_header_set)
elif _CDs & final_header_set:
assert not (_PCs & final_header_set)
# Check that the new wcs is the same as the old.
for k, v in new_wcs_header.items():
if isinstance(v, str):
assert header_from_wcs[k] == v
else:
np.testing.assert_almost_equal(header_from_wcs[k], v)
def copy_ginga_files(verbose=False):
"""Copy Ginga configuration files to HOME directory.
Parameters
----------
verbose : bool
Print info to screen.
"""
# NOTE: There is no need to copy plugins here anymore.
#
# Copy configuration files.
dstpath = os.path.join(_home, '.ginga')
if not os.path.exists(dstpath):
os.makedirs(dstpath)
for filename in get_pkg_data_filenames('config', pattern='*.*'):
_do_copy(filename, os.path.join(dstpath, os.path.basename(filename)),
verbose=verbose)
def copy_ginga_files(verbose=False):
"""Copy Ginga configuration files to HOME directory.
Parameters
----------
verbose : bool
Print info to screen.
"""
# NOTE: There is no need to copy plugins here anymore.
#
# Copy configuration files.
dstpath = os.path.join(_home, '.ginga')
if not os.path.exists(dstpath):
os.makedirs(dstpath)
for filename in get_pkg_data_filenames('config', pattern='*.*'):
_do_copy(filename,
os.path.join(dstpath, os.path.basename(filename)),
verbose=verbose)
def get_path_to_file(*data_name: str, package=None):
"""Get path to file.
Similar to :func:`~astropy.utils.data.get_pkg_data_filename`, but only
gets the path to the file, does not check if the file exists.
The package directory must exist.
Parameters
----------
*data_name : tuple of str
the path, without folder delimiters (which are platform specific)
relative to `package`.
One of the following:
* The name of a directory included in the source
distribution. The path is relative to the module
calling this function. For example, if calling from
``astropy.pkname``, use ``'data'`` to get the
files in ``astropy/pkgname/data``.
* Remote URLs are not currently supported.
package : str, optional
If specified, look for a file relative to the given package, rather
than the default of looking relative to the calling module's package.
Returns
-------
filename : str
A file path on the local file system corresponding to the data
requested in ``data_name``.
"""
# TODO more robust system
fps = list(get_pkg_data_filenames(".", package=package))
filename = pathlib.Path(fps[0]).parent.joinpath(*data_name)
return str(filename)
def setup(self):
self._file_list = list(get_pkg_data_filenames("data/spectra",
pattern="*.hdr"))
def setup(self):
# get the list of the hdr files that we want to test
self._file_list = list(get_pkg_data_filenames("data/maps", pattern="*.hdr"))
def test_open_files():
for filename in get_pkg_data_filenames('data', pattern='*.xml'):
if filename.endswith('custom_datatype.xml'):
continue
parse(filename)
def test_read():
# Check that all test files including reference files are readable
files = get_pkg_data_filenames('data')
for f in files:
with open(f) as f:
DS9Parser(f.read(), errors='warn')
def test_open_files():
for filename in get_pkg_data_filenames('data', pattern='*.xml'):
if filename.endswith('custom_datatype.xml'):
continue
parse(filename, pedantic=False)
import os
import pytest
import numpy as np
from astropy.utils.data import get_pkg_data_filenames, get_pkg_data_contents
from astropy.utils.misc import NumpyRNGContext
from astropy import wcs
from astropy.wcs.wcs import FITSFixedWarning
# use the base name of the file, because everything we yield
# will show up in the test name in the pandokia report
hdr_map_file_list = [
os.path.basename(fname)
for fname in get_pkg_data_filenames("data/maps", pattern="*.hdr")
]
# Checking the number of files before reading them in.
# OLD COMMENTS:
# AFTER we tested with every file that we found, check to see that we
# actually have the list we expect. If N=0, we will not have performed
# any tests at all. If N < n_data_files, we are missing some files,
# so we will have skipped some tests. Without this check, both cases
# happen silently!
def test_read_map_files():
# how many map files we expect to see
n_map_files = 28
def test_read():
# Check that all test files including reference files are readable
files = get_pkg_data_filenames('data')
for f in files:
with open(f) as f:
DS9Parser(f.read(), errors='warn')
def test_read():
# Check that all test files including reference files are readable
files = get_pkg_data_filenames('data')
for f in files:
read_ds9(f)
def test_read():
# Check that all test files including reference files are readable
files = get_pkg_data_filenames('data')
for f in files:
read_ds9(f, errors='warn')
def setup(self):
# get the list of the hdr files that we want to test
self._file_list = list(get_pkg_data_filenames(
"data/maps", pattern="*.hdr"))
def setup(self):
self._file_list = list(get_pkg_data_filenames("data/spectra",
pattern="*.hdr"))
import os
import pytest
import numpy as np
from astropy.utils.data import get_pkg_data_filenames, get_pkg_data_contents
from astropy.utils.misc import NumpyRNGContext
from astropy import wcs
# hdr_map_file_list = list(get_pkg_data_filenames("maps", pattern="*.hdr"))
# use the base name of the file, because everything we yield
# will show up in the test name in the pandokia report
hdr_map_file_list = [os.path.basename(fname) for fname in get_pkg_data_filenames("data/maps", pattern="*.hdr")]
# Checking the number of files before reading them in.
# OLD COMMENTS:
# AFTER we tested with every file that we found, check to see that we
# actually have the list we expect. If N=0, we will not have performed
# any tests at all. If N < n_data_files, we are missing some files,
# so we will have skipped some tests. Without this check, both cases
# happen silently!
def test_read_map_files():
# how many map files we expect to see
n_map_files = 28
assert len(hdr_map_file_list) == n_map_files, (
