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(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)
# This point only reached if on-disk catalog can be reused
msg = "%s: on-disk catalog exists and MD5 hashes match. Yay!"
logging.debug(msg % self.path)
except (KeyError, IOError, ValueError):
msg = ("%s: could not reuse an existing, on-disk cached catalog; "
"SExtractor must be run") % self.path
logging.debug(msg)
# Redirect standard and error outputs to null device
with open(os.devnull, 'wt') as fd:
logging.info("%s: running SExtractor" % self.path)
self.catalog_path = \
astromatic.sextractor(self.path, options = options,
stdout = fd, stderr = fd)
logging.debug("%s: SExtractor OK" % self.path)
try:
# Update the FITS header with the path and MD5; give up
# silently in case we do not have permissions to do it
# (IOError) or if the length of the HIERARCH keyword, equal
# sign and value is longer than 80 characters (ValueError,
# see FITSImage.update_keyword() for details). The cast to
# str is needed because PyFITS has complained sometimes
# about "illegal values" if it receives a Unicode string.
self.update_keyword(keywords.sex_catalog, str(self.catalog_path))
self.update_keyword(keywords.sex_md5sum, sex_md5sum)
except (IOError, ValueError):
pass
# This point only reached if on-disk catalog can be reused
msg = "%s: on-disk catalog exists and MD5 hashes match. Yay!"
logging.debug(msg % self.path)
except (KeyError, IOError, ValueError):
msg = ("%s: could not reuse an existing, on-disk cached catalog; "
"SExtractor must be run") % self.path
logging.debug(msg)
# Redirect standard and error outputs to null device
with open(os.devnull, 'wt') as fd:
logging.info("%s: running SExtractor" % self.path)
self.catalog_path = \
astromatic.sextractor(self.path, options = options,
stdout = fd, stderr = fd)
logging.debug("%s: SExtractor OK" % self.path)
try:
# Update the FITS header with the path and MD5; give up
# silently in case we do not have permissions to do it
# (IOError) or if the length of the HIERARCH keyword, equal
# sign and value is longer than 80 characters (ValueError,
# see FITSImage.update_keyword() for details). The cast to
# str is needed because PyFITS has complained sometimes
# about "illegal values" if it receives a Unicode string.
self.update_keyword(keywords.sex_catalog,
str(self.catalog_path))
self.update_keyword(keywords.sex_md5sum, sex_md5sum)
except (IOError, ValueError):