def test_load_globals():
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = 'tests/test_files/1904-66_SIN.fits'
aux_files = sf.get_aux_files('tests/test_files/1904-66_SIN.fits')
sfinder.load_globals(filename)
if sfinder.global_data.img is None: raise AssertionError()
del sfinder
sfinder = sf.SourceFinder(log=log)
sfinder.load_globals(filename, bkgin=aux_files['bkg'], rms=1, mask=aux_files['mask'])
# region isn't available due to healpy not being installed/required
if sfinder.global_data.region is None: raise AssertionError()
del sfinder
sfinder = sf.SourceFinder(log=log)
sfinder.load_globals(filename, rmsin=aux_files['rms'], mask='derp', do_curve=False)
if sfinder.global_data.region is not None: raise AssertionError()
img = sfinder._load_aux_image(sfinder.global_data.img, filename)
if img is None: raise AssertionError()
del sfinder
sfinder = sf.SourceFinder(log=log)
aux_files = sf.get_aux_files('tests/test_files/1904-66_SIN.fits')
from AegeanTools.regions import Region
sfinder.load_globals(filename, rms=1, mask=Region())
if sfinder.global_data.region is None: raise AssertionError()
def test_find_and_prior_parallel():
log = logging.getLogger("Aegean")
cores = sf.check_cores(2)
# don't bother re-running these tests if we have just 1 core
if cores == 1:
return
filename = 'tests/test_files/1904-66_SIN.fits'
# vanilla source finding
sfinder = sf.SourceFinder(log=log)
found = sfinder.find_sources_in_image(filename, cores=cores)
if not (len(found) == 68): raise AssertionError()
# now with some options
aux_files = sf.get_aux_files(filename)
del sfinder
sfinder = sf.SourceFinder(log=log)
_ = sfinder.find_sources_in_image(filename, doislandflux=True, outfile=open('dlme', 'w'), nonegative=False,
rmsin=aux_files['rms'], bkgin=aux_files['bkg'],
mask=aux_files['mask'], cores=cores)
_ = sfinder.priorized_fit_islands(filename, catalogue=found, doregroup=True, cores=cores, outfile=open('dlme','w'))
os.remove('dlme')
del sfinder
sfinder = sf.SourceFinder(log=log)
sfinder.find_sources_in_image('tests/test_files/1904-66_SIN_neg.fits', doislandflux=True, nonegative=False, cores=cores)
def test_island_contours():
"""Test that island contours are correct"""
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = 'tests/test_files/synthetic_test.fits'
nsrc = 98
nisl = 97
ntot = nsrc + nisl
# vanilla source finding
found = sfinder.find_sources_in_image(filename,
cores=1,
rms=0.5,
bkg=0,
doislandflux=True)
components, islands, simples = classify_catalog(found)
isle_0_contour = np.array([(41, 405), (41, 406), (41, 407), (42, 407),
(42, 408), (42, 409), (43, 409), (43, 410),
(44, 410), (45, 410), (46, 410), (47, 410),
(47, 409), (48, 409), (48, 408), (49, 408),
(49, 407), (49, 406), (49, 405), (48, 405),
(48, 404), (48, 403), (47, 403), (46, 403),
(45, 403), (44, 403), (43, 403), (43, 404),
(42, 404), (42, 405)])
if not np.all(np.array(islands[0].contour) == isle_0_contour):
raise AssertionError("Island contour for island 0 is incoorect")
return
def test_esimate_lmfit_parinfo():
"""Test estimate_lmfit_parinfo"""
log = logging.getLogger("Aegean")
# log.setLevel(logging.DEBUG)
sfinder = sf.SourceFinder(log=log)
data = np.zeros(shape=(3, 3))
rmsimg = np.ones(shape=(3, 3))
beam = Beam(1, 1, 0)
# should hit isnegative
data[1, 1] = -6
# should hit outerclip is None
outerclip = None
# should run error because curve is the wrong shape
curve = np.zeros((3, 4))
try:
sfinder.estimate_lmfit_parinfo(data=data,
rmsimg=rmsimg,
curve=curve,
beam=beam,
innerclip=5,
outerclip=outerclip)
except AssertionError as e:
e.message = 'Passed'
else:
raise AssertionError(
"estimate_lmfit_parinfo should err when curve.shape != data.shape")
return
def test_psf_with_nans():
"""Test that a psf map with nans doesn't create a crash"""
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = "tests/test_files/synthetic_test.fits"
psf = "tests/test_files/synthetic_test_psf.fits"
# create a test psf map with all major axis being nans
hdu = fits.open(psf)
print(hdu[0].data.shape)
hdu[0].data[0, :, :] = np.nan
hdu.writeto('dlme_psf.fits')
try:
found = sfinder.find_sources_in_image(filename,
cores=1,
rms=0.5,
bkg=0,
imgpsf='dlme_psf.fits')
except AssertionError as e:
os.remove('dlme_psf.fits')
if 'major' in e.args[0]:
raise AssertionError("Broken on psf maps with nans")
else:
raise
else:
os.remove('dlme_psf.fits')
return
def test_find_and_prior_sources():
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = 'tests/test_files/small.fits'
# vanilla source finding
found = sfinder.find_sources_in_image(filename, cores=1)
if not (len(found) == 2): raise AssertionError()
# now with some options
aux_files = sf.get_aux_files(filename)
found2 = sfinder.find_sources_in_image(filename, doislandflux=True, outfile=open('dlme', 'w'), nonegative=False,
rmsin=aux_files['rms'], bkgin=aux_files['bkg'],
mask=aux_files['mask'], cores=1, docov=False)
if not (len(found2) == 4): raise AssertionError()
isle1 = found2[1]
if not (isle1.int_flux > 0): raise AssertionError()
if not (isle1.max_angular_size > 0): raise AssertionError()
# we should have written some output file
if not (os.path.exists('dlme')): raise AssertionError()
os.remove('dlme')
# pprocess is broken in python3 at the moment so just use 1 core.
if six.PY3:
cores = 1
else:
cores = 2
# this should find one less source as one of the source centers is outside the image.
priorized = sfinder.priorized_fit_islands(filename, catalogue=found, doregroup=False, ratio=1.2, cores=cores, docov=False)
if not (len(priorized) == 2): raise AssertionError()
# this also gives 62 sources even though we turn on regroup
priorized = sfinder.priorized_fit_islands(filename, catalogue=found, doregroup=True, cores=1, outfile=open('dlme','w'), stage=1)
if not (len(priorized) == 2): raise AssertionError()
if not (len(sfinder.priorized_fit_islands(filename, catalogue=[])) == 0): raise AssertionError()
# we should have written some output file
if not (os.path.exists('dlme')): raise AssertionError()
os.remove('dlme')
def find_sources_in_image(imagename,
max_summits=5,
nsigma=10,
usebane=True,
region=None,
cores=16):
"""
sources,rmsimage,bgimage=find_sources_in_image(imagename, max_summits=5, nsigma=10, usebane=True, region=None, cores=16)
runs aegean.find_sources_in_image
but first runs BANE to get the BG/rms estimates
if region is supplied (.mim format) only sources inside that will be identified
"""
if usebane:
rmsimage, bgimage = get_rms_background(imagename, cores=cores)
else:
rmsimage, bgimage = None, None
sf = source_finder.SourceFinder(log=logging.getLogger('fluxmatch'))
sources = sf.find_sources_in_image(imagename,
max_summits=max_summits,
innerclip=nsigma,
rmsin=rmsimage,
bkgin=bgimage,
mask=region,
cores=cores)
return sources, rmsimage, bgimage
def dont_test_find_and_prior_parallel():
"""Test find/piroirze with parallel operation"""
log = logging.getLogger("Aegean")
cores = 1
filename = 'tests/test_files/synthetic_test.fits'
# vanilla source finding
log.info("basic fitting (no bkg/rms")
sfinder = sf.SourceFinder(log=log)
found = sfinder.find_sources_in_image(filename,
cores=cores,
bkg=0,
rms=0.5)
if not (len(found) == 98):
raise AssertionError('found {0} sources'.format(len(found)))
# now with some options
aux_files = sf.get_aux_files(filename)
del sfinder
log.info("fitting with supplied bkg/rms and 2 cores")
cores = 2
sfinder = sf.SourceFinder(log=log)
_ = sfinder.find_sources_in_image(filename,
doislandflux=True,
outfile=open('dlme', 'w'),
nonegative=False,
rmsin=aux_files['rms'],
bkgin=aux_files['bkg'],
mask=aux_files['mask'],
cores=cores)
log.info('now priorised fitting')
_ = sfinder.priorized_fit_islands(filename,
catalogue=found,
doregroup=True,
cores=cores,
outfile=open('dlme', 'w'))
os.remove('dlme')
del sfinder
log.info('fitting negative sources')
sfinder = sf.SourceFinder(log=log)
sfinder.find_sources_in_image('tests/test_files/1904-66_SIN_neg.fits',
doislandflux=True,
nonegative=False,
cores=cores)
def test_save_files():
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = 'tests/test_files/small.fits'
sfinder.save_background_files(image_filename=filename, outbase='dlme')
for ext in ['bkg', 'rms', 'snr', 'crv']:
if not (os.path.exists("dlme_{0}.fits".format(ext))): raise AssertionError()
os.remove("dlme_{0}.fits".format(ext))
def test_save_image():
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = 'tests/test_files/small.fits'
_ = sfinder.find_sources_in_image(filename, cores=1, max_summits=0, blank=True)
bfile = 'dlme_blanked.fits'
sfinder.save_image(bfile)
if not (os.path.exists(bfile)): raise AssertionError()
os.remove(bfile)
def test_misc():
"""Test some random things"""
sf.IslandFittingData()
sf.DummyLM()
sf.SourceFinder(ignored=None, log=log)
def test_find_and_prior_sources():
"""Test find sources and prior sources"""
log = logging.getLogger("Aegean")
sfinder = sf.SourceFinder(log=log)
filename = 'tests/test_files/synthetic_test.fits'
nsrc = 98
nisl = 97
ntot = nsrc + nisl
# vanilla source finding
found = sfinder.find_sources_in_image(filename, cores=1, rms=0.5, bkg=0)
if not (len(found) == nsrc):
raise AssertionError("Found the wrong number of sources {0}".format(
len(found)))
# source finding but not fitting
found = sfinder.find_sources_in_image(filename,
cores=1,
max_summits=0,
rms=0.5,
bkg=0)
if not (len(found) == nsrc):
raise AssertionError("Found the wrong number of sources {0}".format(
len(found)))
# now with some options
aux_files = sf.get_aux_files(filename)
found2 = sfinder.find_sources_in_image(filename,
doislandflux=True,
outfile=open('dlme', 'w'),
nonegative=False,
rmsin=aux_files['rms'],
bkgin=aux_files['bkg'],
mask=aux_files['mask'],
cores=1,
docov=False)
if not (len(found2) == ntot):
raise AssertionError("Found the wrong number of sources {0}".format(
len(found2)))
isle1 = found2[1]
if not (isle1.int_flux > 0):
raise AssertionError()
if not (isle1.max_angular_size > 0):
raise AssertionError()
# we should have written some output file
if not (os.path.exists('dlme')):
raise AssertionError()
os.remove('dlme')
# some more tests, now using multiple cores
cores = 2
priorized = sfinder.priorized_fit_islands(filename,
catalogue=found,
doregroup=False,
ratio=1.2,
cores=cores,
rmsin=aux_files['rms'],
bkgin=aux_files['bkg'],
docov=False)
if not (len(priorized) == nsrc):
raise AssertionError("Found the wrong number of sources {0}".format(
len(priorized)))
priorized = sfinder.priorized_fit_islands(filename,
catalogue=found,
doregroup=True,
cores=1,
rmsin=aux_files['rms'],
bkgin=aux_files['bkg'],
outfile=open('dlme', 'w'),
stage=1)
if not (len(priorized) == nsrc):
raise AssertionError("Found the wrong number of sources {0}".format(
len(priorized)))
if not (len(sfinder.priorized_fit_islands(filename, catalogue=[])) == 0):
raise AssertionError()
# we should have written some output file
if not (os.path.exists('dlme')):
raise AssertionError("Failed to creat outputfile")
os.remove('dlme')
def test_misc():
sf.IslandFittingData()
sf.DummyLM()
sf.SourceFinder(ignored=None, log=log)
