def test_sextractor_not_installed(self, which_mock):
which_mock.return_value = []
with self.assertRaises(astromatic.SExtractorNotInstalled):
astromatic.sextractor_version()
which_mock.assert_has_calls(
[mock.call('sextractor'),
mock.call('sex')])
def test_sextractor_version(self):
# We have no other way of knowing the SExtractor version that is
# installed on the system than running it ourselves with the --version
# option and examine its output: if sextractor_version() returns the
# tuple (2, 8, 6), for example, that means that the SExtractor version
# number must contain the string '2.8.6'. What we are doing, basically,
# is to test the functionality the other way around: we take the tuple
# that sextractror_version() outputs, transform it back to a string and
# verify that it corresponds to what the --version option prints.
try:
executable = methods.which(*astromatic.SEXTRACTOR_COMMANDS)[0]
except IndexError:
msg = "SExtractor not found in the current environment"
raise astromatic.SExtractorNotInstalled(msg)
with tempfile.TemporaryFile() as fd:
args = [executable, '--version']
subprocess.check_call(args, stdout=fd)
fd.seek(0)
# For example: "SExtractor version 2.5.0 (2006-07-14)"
stdout = '\n'.join(fd.readlines())
version = astromatic.sextractor_version()
# From, for example, (2, 5, 0) to '2.5.0'
version_str = '.'.join(str(x) for x in version)
self.assertTrue(version_str in stdout)
# SExtractorNotInstalled must be raised if no SExtractor executable is
# detected. In order to simulate this, mock os.environ and clear the
# 'PATH' environment variable. In this manner, as the list of paths to
# directories where executables may be found is empty, SExtractor (and
# any other command) will appear as not installed on the system.
environment_copy = copy.deepcopy(os.environ)
with mock.patch.object(os, 'environ', environment_copy) as mocked:
mocked['PATH'] = ''
with self.assertRaises(astromatic.SExtractorNotInstalled):
astromatic.sextractor_version()
def test_sextractor(self):
# Note that, being a third-party program, we cannot write a unit test
# to check that SExtractor works as it should (i.e., that it correctly
# detects astronomical sources on FITS images): that is something that
# Emmanuel Bertin, its developer, certainly takes care of. What we must
# test for is whether astromatic.sextractor(), our Python wrapper to
# call SExtractor, works as we expect and raises the appropriate errors
# when something goes wrong. Nothing less, nothing more.
# First, the most probable scenario: our wrapper should run SExtractor
# on any FITS image that it receives (here we use some downloaded from
# the STScI Digitized Sky Survey) and return the path to the output
# catalog, which astromatic.Catalog should be always able to parse.
kwargs = dict(stdout=open(os.devnull), stderr=open(os.devnull))
for img_path in dss_images.TEST_IMAGES:
catalog_path = astromatic.sextractor(img_path, **kwargs)
try:
Catalog(catalog_path)
finally:
os.unlink(catalog_path)
# SExtractorNotInstalled must be raised if no SExtractor executable is
# detected. In order to simulate this, mock os.environ and clear the
# 'PATH' environment variable. In this manner, as the list of paths to
# directories where executables may be found is empty, SExtractor (and
# any other command) will appear as not installed on the system.
environment_copy = copy.deepcopy(os.environ)
with mock.patch.object(os, 'environ', environment_copy) as mocked:
mocked['PATH'] = ''
with self.assertRaises(astromatic.SExtractorNotInstalled):
astromatic.sextractor(img_path)
# IOError is raised if any of the four SExtractor configuration files
# is not readable or does no exist. To test that, mock the module-level
# variables so that they first refer to an unreadable file and later to
# a nonexistent one.
for variable in self.SEXTRACTOR_MODULE_VARS:
path = eval('astromatic.%s' % variable)
ext = os.path.splitext(path)[1]
copy_path = get_nonexistent_path(ext=ext)
shutil.copy2(path, copy_path)
with mock.patch.object(astromatic, variable, copy_path):
# chmod u-r
mode = stat.S_IMODE(os.stat(copy_path)[stat.ST_MODE])
mode ^= stat.S_IRUSR
os.chmod(copy_path, mode)
args = IOError, astromatic.sextractor, img_path
self.assertFalse(os.access(copy_path, os.R_OK))
self.assertRaises(*args)
os.unlink(copy_path)
self.assertFalse(os.path.exists(copy_path))
self.assertRaises(*args)
# SExtractorUpgradeRequired must be raised if the version of SExtractor
# that is installed on the system is older than that defined in the
# SEXTRACTOR_REQUIRED_VERSION module-level variable. We cannot (easily,
# at least) change the version that is installed, but we can test for
# this by changing the value of the required version, setting it to a
# tuple that is greater than the installed version of SExtractor.
# From, for example, (2, 8, 6) to (2, 8, 7)
version = list(astromatic.sextractor_version())
version[-1] += 1
version = tuple(version)
with mock.patch.object(astromatic, 'SEXTRACTOR_REQUIRED_VERSION',
version):
with self.assertRaises(astromatic.SExtractorUpgradeRequired):
astromatic.sextractor(img_path)
# The SExtractorError exception is raised if anything goes wrong during
# the execution of SExtractor (in more technical terms, if its return
# code is other than zero). For example, the FITS image may not exist,
# or a non-numerical value may be assigned to a parameter that expects
# one, or we could try to run SExtractor on a FITS extension that does
# not exist. These three are just examples: SExtractor may fail for
# many different reasons that we cannot even foresee.
# (1) Try to run SExtractor on a non-existent image
kwargs = dict(stdout=open(os.devnull), stderr=open(os.devnull))
nonexistent_path = get_nonexistent_path(ext='.fits')
with self.assertRaises(astromatic.SExtractorError):
astromatic.sextractor(nonexistent_path, **kwargs)
# (2) The DETECT_MINAREA parameter (minimum number of pixels above the
# threshold needed to trigger detection) expects an integer. Assigning
# to it a string will cause SExtractor to complain ("keyword out of
# range") and abort its execution.
kwargs['options'] = dict(DETECT_MINAREA='Y')
with self.assertRaises(astromatic.SExtractorError):
astromatic.sextractor(img_path, **kwargs)
del kwargs['options']
# (3) Try to run SExtractor on a nonexistent FITS extension.
hdulist = pyfits.open(img_path, mode='readonly')
nextensions = len(hdulist)
hdulist.close()
kwargs['ext'] = nextensions + 1
with self.assertRaises(astromatic.SExtractorError):
astromatic.sextractor(img_path, **kwargs)
# TypeError raised if 'options' is not a dictionary
kwargs = dict(options=['DETECT_MINAREA', '5'])
with self.assertRaises(TypeError):
astromatic.sextractor(img_path, **kwargs)
# ... or if any of its elements is not a string.
kwargs['options'] = {'DETECT_MINAREA': 125}
with self.assertRaises(TypeError):
astromatic.sextractor(img_path, **kwargs)
# TypeError also raised if 'ext' is not an integer...
kwargs = dict(ext=0.56)
with self.assertRaises(TypeError):
astromatic.sextractor(img_path, **kwargs)
# ... even if it is a float but has nothing after the decimal point
# (for which the built-in is_integer() function would return True).
kwargs = dict(ext=0.0)
with self.assertRaises(TypeError):
astromatic.sextractor(img_path, **kwargs)
def test_sextractor_version(self, check_output_mock):
check_output_mock.return_value = "SExtractor version 2.19.5 (2014-03-19)\n"
self.assertEqual((2, 19, 5), astromatic.sextractor_version())
check_output_mock.assert_called_once()
match = re.match(regexp, version)
if match is None:
msg = "cannot extract version from '%s' (%s)" % (version, module)
raise Exception(msg)
else:
version = match.group(0)
return str_to_version(version)
# For each module whose minimum version has been defined in requirements.txt,
# create an import hook and add it to sys.meta_path, which is searched before
# any implicit default finders or sys.path.
for module, version in [
("numpy", (1, 7, 1)),
("aplpy", (0, 9, 9)),
("scipy", (0, 12, 0)),
("matplotlib", (1, 2, 1)),
("mock", (1, 0, 1)),
("pyfits", (3, 1, 2)),
("pyraf", (2, 1, 1)),
("uncertainties", (2, 4, 1)),
]:
hook = RequireModuleVersionHook(module, version, get__version__)
sys.meta_path.append(hook)
# If the minimum version is not met, raise SExtractorUpgradeRequired as
# soon as possible, instead of waiting until we attempt to run SExtractor.
if astromatic.sextractor_version() < astromatic.SEXTRACTOR_REQUIRED_VERSION:
raise astromatic.SExtractorUpgradeRequired()
regexp = "\d+(\.\d+)+"
match = re.match(regexp, version)
if match is None:
msg = "cannot extract version from '%s' (%s)" % (version, module)
raise Exception(msg)
else:
version = match.group(0)
return str_to_version(version)
# For each module whose minimum version has been defined in requirements.txt,
# create an import hook and add it to sys.meta_path, which is searched before
# any implicit default finders or sys.path.
for module, version in [('numpy', (1, 7, 1)), ('aplpy', (0, 9, 9)),
('scipy', (0, 12, 0)), ('matplotlib', (1, 2, 1)),
('mock', (1, 0, 1)), ('pyfits', (3, 1, 2)),
('pyraf', (2, 1, 1)), ('uncertainties', (2, 4, 1))]:
hook = RequireModuleVersionHook(module, version, get__version__)
sys.meta_path.append(hook)
# If the minimum version is not met, raise SExtractorUpgradeRequired as
# soon as possible, instead of waiting until we attempt to run SExtractor.
sextractor_version = astromatic.sextractor_version()
sextractor_minimum = astromatic.SEXTRACTOR_REQUIRED_VERSION
if not sextractor_version >= sextractor_minimum:
msg = "SExtractor >= %s is required, found %s"
args = (version_to_str(sextractor_minimum),
version_to_str(sextractor_version))
raise astromatic.SExtractorUpgradeRequired(msg % args)
