def test_from_header():
fname = 'tests/test_files/1904-66_SIN.fits'
header = fits.getheader(fname)
helper = WCSHelper.from_header(header)
if helper.beam is None: raise AssertionError()
del header['BMAJ'], header['BMIN'], header['BPA']
helper = WCSHelper.from_header(header)
if helper.beam is not None: raise AssertionError()
def test_from_header():
"""Test that we can make a beam from a fitsheader"""
fname = 'tests/test_files/1904-66_SIN.fits'
header = fits.getheader(fname)
helper = WCSHelper.from_header(header)
if helper.beam is None: raise AssertionError()
del header['BMAJ'], header['BMIN'], header['BPA']
helper = WCSHelper.from_header(header)
if helper.beam is not None: raise AssertionError()
def test_get_pixbeam():
"""Test get_pixbeam"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
beam = helper.get_pixbeam_pixel(0, 0)
verify_beam(beam)
helper.lat = None
beam = helper.get_beam(285, -66)
verify_beam(beam)
helper.lat = -65
beam = helper.get_beam(285, -66)
verify_beam(beam)
area = helper.get_beamarea_pix(285, -66)
if not (area > 0): raise AssertionError()
area = helper.get_beamarea_deg2(285, -66)
if not (area >0): raise AssertionError()
beam = helper.get_pixbeam(285, -66)
verify_beam(beam)
beam = helper.get_pixbeam(None, None)
verify_beam(beam)
def test_get_pixbeam():
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
beam = helper.get_pixbeam_pixel(0, 0)
verify_beam(beam)
helper.lat = None
beam = helper.get_beam(285, -66)
verify_beam(beam)
helper.lat = -65
beam = helper.get_beam(285, -66)
verify_beam(beam)
area = helper.get_beamarea_pix(285, -66)
if not (area > 0): raise AssertionError()
area = helper.get_beamarea_deg2(285, -66)
if not (area > 0): raise AssertionError()
beam = helper.get_pixbeam(285, -66)
verify_beam(beam)
beam = helper.get_pixbeam(None, None)
verify_beam(beam)
def main():
# TODO:
# make the noise vary as as if there are a bunch of tessellated observations
# Each obs should have a different noise contribution
# print "Creating noise with imprinted variation"
print "creating rms map"
noise_map = fits.open('bane_smooth.fits')
noise_map[0].data = np.float32(0.1*(1+2*noise_map[0].data))
noise_map.writeto('rms.fits', overwrite=True)
print "Creating noise map"
# gaussian noise with sigma = 1
np.random.seed(69084124)
noise = np.random.normal(0, 1, noise_map[0].data.shape)
print "imprinting pattern onto noise"
# rescale the noise so that some parts of the map have 3x the noise of others
# and imprint a pattern into the noise
noise_map[0].data *= noise
noise_map.writeto('temp.fits', overwrite=True)
print "wrote temp.fits"
print "Convolving with variable psf"
wcsh = WCSHelper.from_file('bane_smooth.fits')
psfh = PSFHelper('psf.fits', wcsh)
smoothed = convolve(noise, psfh)
print "writing file"
noise_map[0].data = np.float32(smoothed)
noise_map.writeto('noise.fits', overwrite=True)
def test_psf_funcs():
"""
For a SIN projected image, test that the beam/psf calculations are consistent at different points on the sky
"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
header = helper.wcs.to_header()
refpix = header['CRPIX2'], header['CRPIX1'] # note x/y swap
refcoord = header['CRVAL1'], header['CRVAL2']
beam_ref_coord = helper.get_skybeam(*refcoord)
beam_ref_pix = helper.get_skybeam(*helper.pix2sky(refpix))
msg = 'sky beams at ref coord/pix disagree'
if not abs(beam_ref_coord.a - beam_ref_pix.a) < 1e-5:
raise AssertionError(msg)
if not abs(beam_ref_coord.b - beam_ref_pix.b) < 1e-5:
raise AssertionError(msg)
if not abs(beam_ref_coord.pa - beam_ref_pix.pa) < 1e-5:
raise AssertionError(msg)
psf_zero = helper.get_psf_sky2pix(0, 0)
psf_refcoord = helper.get_psf_sky2pix(*refcoord)
diff = np.subtract(psf_zero, psf_refcoord)
if not np.all(diff < 1e-5):
raise AssertionError("psf varies in pixel coordinates (it should not)")
diff = np.subtract(psf_refcoord,
(helper._psf_a, helper._psf_b, helper._psf_theta))
if not np.all(diff < 1e-5):
raise AssertionError("psf varies in pixel coordinates (it should not)")
return
def test_from_header():
"""Test that we can make a beam from a fitsheader"""
fname = 'tests/test_files/1904-66_SIN.fits'
header = fits.getheader(fname)
helper = WCSHelper.from_header(header)
if helper.beam is None: raise AssertionError()
del header['BMAJ'], header['BMIN'], header['BPA']
# Raise an error when the beam information can't be determined
try:
_ = WCSHelper.from_header(header)
except AssertionError as e:
pass
else:
raise AssertionError(
"Header with no beam information should thrown an exception.")
return
def test_ellipse_round_trip():
"""
Converting an ellipse from pixel to sky coords and back again should give the
original ellipse (within some tolerance).
"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
a = 2 * helper.beam.a
b = helper.beam.b
pa = helper.beam.pa + 45
ralist = list(range(-180, 180, 10))
# SIN projection isn't valid for all decs
declist = list(range(-85, -10, 10))
ras, decs = np.meshgrid(ralist, declist)
for _, (ra, dec) in enumerate(zip(ras.ravel(), decs.ravel())):
if ra < 0:
ra += 360
x, y, sx, sy, theta = helper.sky2pix_ellipse((ra, dec), a, b, pa)
ra_f, dec_f, major, minor, pa_f = helper.pix2sky_ellipse((x, y), sx,
sy, theta)
assert_almost_equal(ra, ra_f)
assert_almost_equal(dec, dec_f)
if not (abs(a - major) / a < 0.05): raise AssertionError()
if not (abs(b - minor) / b < 0.05): raise AssertionError()
if not (abs(pa - pa_f) < 1): raise AssertionError()
def test_galactic_coords():
"""Test that we can work with galactic coordinates"""
fname = 'tests/test_files/1904-66_SIN.lb.fits'
header = fits.getheader(fname)
try:
helper = WCSHelper.from_header(header)
except ValueError as e:
raise AssertionError("galactic coordinates break WCSHelper")
return
def test_psf_files():
"""Test that using external psf files works properly"""
fname = 'tests/test_files/1904-66_SIN.fits'
psfname = 'tests/test_files/1904-66_SIN_psf.fits'
helper = WCSHelper.from_file(fname, psf_file=psfname)
# The psf image has only 19x19 pix and this ra/dec is
a, b, pa = helper.get_psf_sky2sky(290., -63.)
if not np.all(np.isfinite((a, b, pa))):
raise AssertionError("Beam contains nans")
def test_vector_round_trip():
"""
Converting a vector from pixel to sky coords and back again should give the
original vector (within some tolerance).
"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
initial = [1, 45] # r,theta = 1,45 (degrees)
ref = helper.refpix
ra, dec, dist, ang = helper.pix2sky_vec(ref, *initial)
_, _ , r, theta = helper.sky2pix_vec([ra, dec], dist, ang)
if not ((abs(r - initial[0]) < 1e-9) and (abs(theta - initial[1]) < 1e-9)): raise AssertionError()
def test_vector_round_trip():
"""
Converting a vector from pixel to sky coords and back again should give the
original vector (within some tolerance).
"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
initial = [1, 45] # r,theta = 1,45 (degrees)
ref = helper.refpix
ra, dec, dist, ang = helper.pix2sky_vec(ref, *initial)
_, _, r, theta = helper.sky2pix_vec((ra, dec), dist, ang)
if not ((abs(r - initial[0]) < 1e-9) and (abs(theta - initial[1]) < 1e-9)):
raise AssertionError()
def test_get_pixbeam():
"""Test get_pixbeam"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
beam = Beam(*helper.get_psf_pix2pix(0, 0))
verify_beam(beam)
beam = helper.get_skybeam(285, -66)
verify_beam(beam)
beam = helper.get_skybeam(285, -66)
verify_beam(beam)
area = helper.get_beamarea_pix(285, -66)
if not (area > 0): raise AssertionError()
area = helper.get_beamarea_deg2(285, -66)
if not (area > 0): raise AssertionError()
def test_ellipse_round_trip():
"""
Converting an ellipse from pixel to sky coords and back again should give the
original ellipse (within some tolerance).
"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
a = 2 * helper.beam.a
b = helper.beam.b
pa = helper.beam.pa + 45
ralist = list(range(-180, 180, 10))
# SIN projection isn't valid for all decs
declist = list(range(-85, -10, 10))
ras, decs = np.meshgrid(ralist, declist)
for _, (ra, dec) in enumerate(zip(ras.ravel(), decs.ravel())):
if ra < 0:
ra += 360
x, y, sx, sy, theta = helper.sky2pix_ellipse([ra, dec], a, b, pa)
ra_f, dec_f, major, minor, pa_f = helper.pix2sky_ellipse([x, y], sx, sy, theta)
assert_almost_equal(ra, ra_f)
assert_almost_equal(dec, dec_f)
if not (abs(a-major)/a < 0.05): raise AssertionError()
if not (abs(b-minor)/b < 0.05): raise AssertionError()
if not (abs(pa-pa_f) < 1): raise AssertionError()
def test_sky_sep():
"""Test sky separation"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
dist = helper.sky_sep((0, 0), (1, 1))
if not (dist > 0): raise AssertionError()
def test_from_file():
"""Test that we can load from a file"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
if helper.beam is None: raise AssertionError()
src.island = 102
src.peak_flux = 80 * noise
cat.append(src)
return cat
if __name__ == "__main__":
# configure logging
logging.basicConfig(format="%(module)s:%(levelname)s %(message)s")
log = logging.getLogger("Aegean")
logging_level = logging.DEBUG # if options.debug else logging.INFO
log.setLevel(logging_level)
image, wcs = make_noise_image()
header = wcs.to_header()
header['BMAJ'] = psf[0] / 3600
header['BMIN'] = psf[1] / 3600
header['BPA'] = psf[2]
hdu = fits.HDUList(hdus=[fits.PrimaryHDU(header=header, data=image)])
header = hdu[0].header
cat = make_catalogue()
wcshelper = WCSHelper.from_header(header)
hdu[0].data += AeRes.make_model(cat, image.shape, wcshelper)
hdu.writeto('synthetic_test.fits', overwrite=True)
psf_hdu = make_psf_map(hdu)
psf_hdu.writeto('synthetic_test_psf.fits', overwrite=True)
def test_from_file():
"""Test that we can load from a file"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
if helper.beam is None: raise AssertionError()
print(fmt % ("OuterClip", str(outerclip)))
print(fmt % ("Cores", str(cores)))
print(fmt % ("catalog file", catalog_file))
print(fmt % ("catalog file [point]", catalog_file_point))
print(fmt % ("plot file", plot_file))
print(fmt % ("cutx0", cutx0))
print(fmt % ("cutx1", cutx1))
print(fmt % ("cuty0", cuty0))
print(fmt % ("cuty1", cuty1))
print(fmt % ("fluxmin", fluxmin))
hdu = fits.open(fits_file)[0]
fits_data = hdu.data
fits_header = hdu.header
mywcs_helper = WCSHelper.from_file(fits_file)
log = logging.getLogger(bname)
sf = SourceFinder(log=log)
found = sf.find_sources_in_image( filename = fits_file,\
innerclip = innerclip,\
outerclip = outerclip,\
cores = 5,\
nonegative=False \
#nonegative=True \
)
save_catalog(catalog_file, found)
shape = fits_data.shape
m, n = shape
m0 = int(m * cuty0)
def test_from_file():
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
if helper.beam is None: raise AssertionError()
def test_sky_sep():
"""Test sky separation"""
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
dist = helper.sky_sep([0, 0], [1, 1])
if not (dist > 0): raise AssertionError()
def test_estimate_parinfo_image():
"""Test"""
log = logging.getLogger("Aegean")
#log.setLevel(logging.DEBUG)
wcshelper = WCSHelper.from_file(
filename='tests/test_files/1904-66_SIN.fits')
im = np.zeros(shape=(10, 10), dtype=np.float32) * np.nan
bkg = np.zeros_like(im)
rms = np.ones_like(im)
im[2:5, 2:5] = 6.
im[3, 3] = 8.
islands = sf.find_islands(im, bkg, rms, log=log)
sources = sf.estimate_parinfo_image(islands,
im=im,
rms=rms,
wcshelper=wcshelper,
log=log)
if len(sources) != 1:
raise AssertionError(
"Incorrect number of sources found {0}, expecting 1".format(
len(sources)))
if not sources[0]['components'].value == 1:
raise AssertionError("Found {0} components, expecting 1".format(
sources[0]['components'].value))
if not sources[0]['c0_amp'].value == 8.0:
raise AssertionError("c0_amp is not 8.0 (is {0})".format(
sources[0]['c0_amp'].value))
# test on a negative island
im *= -1.
islands = sf.find_islands(im, bkg, rms, log=log)
sources = sf.estimate_parinfo_image(islands,
im=im,
rms=rms,
wcshelper=wcshelper,
log=log)
if len(sources) != 1:
raise AssertionError(
"Incorrect number of sources found {0}, expecting 1".format(
len(sources)))
if not sources[0]['components'].value == 1:
raise AssertionError("Found {0} components, expecting 1".format(
sources[0]['components'].value))
if not sources[0]['c0_amp'].value == -8.0:
raise AssertionError("c0_amp is not -8.0 (is {0})".format(
sources[0]['c0_amp'].value))
# test on a small island
im[:, :] = np.nan
im[2:4, 2:4] = 6.
im[3, 3] = 8.
islands = sf.find_islands(im, bkg, rms, log=log)
sources = sf.estimate_parinfo_image(islands,
im=im,
rms=rms,
wcshelper=wcshelper,
log=log)
if len(sources) != 1:
raise AssertionError(
"Incorrect number of sources found {0}, expecting 1".format(
len(sources)))
if not sources[0]['components'].value == 1:
raise AssertionError("Found {0} components, expecting 1".format(
sources[0]['components'].value))
if not (sources[0]['c0_flags'].value & flags.FIXED2PSF):
raise AssertionError("FIXED2PSF flag not detected")
def test_sky_sep():
fname = 'tests/test_files/1904-66_SIN.fits'
helper = WCSHelper.from_file(fname)
dist = helper.sky_sep([0, 0], [1, 1])
if not (dist > 0): raise AssertionError()