def test_apertures_all():
"""Test that aperture subpixel sampling works"""
data = np.random.rand(*data_shape)
r = 3.
rtol = 1.e-8
for subpix in [0, 1, 5]:
flux_ref, fluxerr_ref, flag_ref = sep.sum_circle(data,
x,
y,
r,
subpix=subpix)
flux, fluxerr, flag = sep.sum_circann(data, x, y, 0., r, subpix=subpix)
assert_allclose(flux, flux_ref, rtol=rtol)
flux, fluxerr, flag = sep.sum_ellipse(data,
x,
y,
r,
r,
0.,
subpix=subpix)
assert_allclose(flux, flux_ref, rtol=rtol)
flux, fluxerr, flag = sep.sum_ellipse(data,
x,
y,
1.,
1.,
0.,
r=r,
subpix=subpix)
assert_allclose(flux, flux_ref, rtol=rtol)
def sep_phot(exp_data, asteroid_id, ap=10.0):
"""
Measure background of postage stamp and the flux_err of the asteroid
"""
data2 = np.ones(exp_data.shape) * exp_data
# np.copyto(data2, exp_data)
try:
bkg = sep.Background(data2)
except ValueError:
data3 = data2.byteswap(True).newbyteorder()
bkg = sep.Background(data3)
# Directly subtract the background from the data in place
bkg.subfrom(data2)
# calculate the Kron radius for each object, then we perform elliptical aperture photometry within that radius
kronrad, krflag = sep.kron_radius(data2, asteroid_id[_XMID_HEADER], asteroid_id[_YMID_HEADER],
asteroid_id[_A_HEADER],
asteroid_id['b'], asteroid_id[_THETA_HEADER], ap)
flux, fluxerr, flag = sep.sum_ellipse(data2, asteroid_id[_XMID_HEADER], asteroid_id[_YMID_HEADER],
asteroid_id[_A_HEADER], asteroid_id[_B_HEADER],
asteroid_id[_THETA_HEADER], 2.5 * kronrad, subpix=1, err=bkg.globalrms)
return bkg.globalback, flux, fluxerr
def sep_phot(data, ap, th):
"""
Preforms photometry by SEP, similar to source extractor
"""
# Measure a spatially variable background of some image data (np array)
try:
bkg = sep.Background(data) # , mask=mask, bw=64, bh=64, fw=3, fh=3) # optional parameters
except ValueError:
data = data.byteswap(True).newbyteorder()
bkg = sep.Background(data) # , mask=mask, bw=64, bh=64, fw=3, fh=3) # optional parameters
# Directly subtract the background from the data in place
bkg.subfrom(data)
# for the background subtracted data, detect objects in data given some threshold
thresh = th * bkg.globalrms # ensure the threshold is high enough wrt background
objs = sep.extract(data, thresh)
# calculate the Kron radius for each object, then we perform elliptical aperture photometry within that radius
kronrad, krflag = sep.kron_radius(data, objs['x'], objs['y'], objs['a'], objs['b'], objs['theta'], ap)
flux, fluxerr, flag = sep.sum_ellipse(data, objs['x'], objs['y'], objs['a'], objs['b'], objs['theta'],
2.5 * kronrad, subpix=1)
flag |= krflag # combine flags into 'flag'
r_min = 1.75 # minimum diameter = 3.5
use_circle = kronrad * np.sqrt(objs['a'] * objs['b']) < r_min
x = objs['x']
y = objs['y']
cflux, cfluxerr, cflag = sep.sum_circle(data, x[use_circle], y[use_circle],
r_min, subpix=1)
flux[use_circle] = cflux
fluxerr[use_circle] = cfluxerr
flag[use_circle] = cflag
return objs
def test_apertures_exact():
"""Test area as measured by exact aperture modes on array of ones"""
theta = np.random.uniform(-np.pi/2., np.pi/2., naper)
ratio = np.random.uniform(0.2, 1.0, naper)
r = 3.
for dt in SUPPORTED_IMAGE_DTYPES:
data = np.ones(data_shape, dtype=dt)
for r in [0.5, 1., 3.]:
flux, fluxerr, flag = sep.sum_circle(data, x, y, r, subpix=0)
assert_allclose(flux, np.pi*r**2)
rout = r*1.1
flux, fluxerr, flag = sep.sum_circann(data, x, y, r, rout,
subpix=0)
assert_allclose(flux, np.pi*(rout**2 - r**2))
flux, fluxerr, flag = sep.sum_ellipse(data, x, y, 1., ratio,
theta, r=r, subpix=0)
assert_allclose(flux, np.pi*ratio*r**2)
rout = r*1.1
flux, fluxerr, flag = sep.sum_ellipann(data, x, y, 1., ratio,
theta, r, rout, subpix=0)
assert_allclose(flux, np.pi*ratio*(rout**2 - r**2))
def AperaturePhoto(self,filter,objs):
print 'Running Aperature Photometry on %s......'%filter
kronrad, krflag = sep.kron_radius(self.dataList[filter],
objs['x'], objs['y'],
objs['a'], objs['b'],
objs['theta'],
6.0)
flux, fluxerr, flag = sep.sum_ellipse(self.dataList[filter],
objs['x'], objs['y'],
objs['a'], objs['b'],
objs['theta'],
2.5*kronrad, subpix=1,
err=self.bkgRMS[filter])
#use circular aperature photometry if the kronradius is too small. see http://sep.readthedocs.org/en/v0.2.x/apertures.html
r_min = 1.75 # minimum diameter = 3.5
use_circle = kronrad * np.sqrt(objs['a']*objs['b']) < r_min
cflux, cfluxerr, cflag = sep.sum_circle(self.dataList[filter],
objs['x'][use_circle],
objs['y'][use_circle],
r_min, subpix=1,err=self.bkgRMS[filter])
flux[use_circle] = cflux
fluxerr[use_circle] = cfluxerr
flag[use_circle] = cflag
#convert flux to magnitudes using the appropriate zeropoint
#absolute flux measurement (AB for Z-PEG)
mag = -2.5*np.log10(flux)+self.zeroPoints[filter]
#calculate magerr
fluxdown = flux - fluxerr
fluxup = flux + fluxerr
magup = -2.5*np.log10(fluxdown) + self.zeroPoints[filter]
magdown = -2.5*np.log10(fluxup) + self.zeroPoints[filter]
magerr = ((magup - mag) + (mag-magdown))/2.
return mag, magerr
def calc_flux_err(a: float, img_back: ndarray, x: float, y: float,
elongation: float, theta: float, err: ndarray, mask: ndarray,
gain: float) -> float:
"""
Calculate flux error for a source depending on the aperture size; used
by adaptive photometry to calculate the optimal aperture
:param a: aperture size
:param img_back: image with background subtracted
:param x: source centroid X
:param y: source centroid Y
:param elongation: isophotal a/b ratio for the source
:param theta: major axis position angle in radians
:param err: background RMS
:param mask: image mask
:param gain: inverse gain in e-/ADU
:return: flux error for the given aperture
"""
flux, flux_err, flags = sep.sum_ellipse(
img_back, [x], [y], a, a/elongation, theta, 1, err=err, mask=mask,
gain=gain, subpix=0)
if flags:
raise ValueError('flags = {}'.format(flags))
if flux <= 0:
raise ValueError('flux = {}'.format(flux))
return flux_err/flux
def test_apertures_small_ellipse_exact():
"""Regression test for a bug that manifested primarily when x == y."""
data = np.ones(data_shape)
r = 0.3
rtol=1.e-10
flux, fluxerr, flag = sep.sum_ellipse(data, x, x, r, r, 0., subpix=0)
assert_allclose(flux, np.pi*r**2, rtol=rtol)
def catalog(ccd, bgf, catf, db, config, logger):
bg = fits.open(bgf)
im = ccd.data - bg['background'].data
ps = ccd.meta['SCALE'] * ccd.meta.get('REBIN', 1)
bgrms = bg['background'].header['bgrms']
objects = sep.extract(im, 2, err=bgrms, mask=ccd.mask)
logger.info('Found {} sources.'.format(len(objects)))
rap = max(ccd.meta['SEEING'] * 2, 5 / ps)
flux, fluxerr, flag = sep.sum_circle(im,
objects['x'],
objects['y'],
rap,
err=bgrms)
# avoid theta rounding error
theta = np.maximum(np.minimum(objects['theta'], np.pi / 2.00001),
-np.pi / 2.00001)
kronrad, krflag = sep.kron_radius(im, objects['x'], objects['y'],
objects['a'], objects['b'], theta, 6.0)
krflux, krfluxerr, _flag = sep.sum_ellipse(im,
objects['x'],
objects['y'],
objects['a'],
objects['b'],
theta,
2.5 * kronrad,
subpix=1,
err=bgrms)
krflag |= _flag
# an additional background estimate, which should help when there are
# large extended sources in scene: IN TESTS, THIS DID NOT AFFECT RESULTS
# for i in range(len(objects)):
# krflux[i], krfluxerr[i] = bg_subtract2(im, objects[i], krflux[i],
# krfluxerr[i])
# flux[i], fluxerr[i] = bg_subtract2(im, objects[i], flux[i],
# fluxerr[i], r=rap)
if ccd.wcs.wcs.crval[0] == ccd.wcs.wcs.crval[1]:
ra, dec = np.zeros((2, len(objects)))
else:
ra, dec = ccd.wcs.all_pix2world(objects['x'], objects['y'], 0)
tab = Table(
(objects['x'], objects['y'], ra, dec, flux, fluxerr, flag,
objects['a'], objects['b'], theta, kronrad, krflux, krfluxerr,
krflag),
names=('x', 'y', 'ra', 'dec', 'flux', 'fluxerr', 'flag', 'a', 'b',
'theta', 'kronrad', 'krflux', 'krfluxerr', 'krflag'))
hdu = fits.HDUList()
hdu.append(fits.BinTableHDU(tab, name='cat'))
hdu['cat'].header['RADIUS'] = (rap * ps,
'aperture photometry radius, arcsec')
hdu.writeto(catf, overwrite=True)
def plot_light_curves(diff_cube, unique_extracted_objects):
# The diff_cube has to be byte swapped BEFORE being sent as parameter (diff_cube.byteswap(True).newbyteorder()), otherwise the method is not goint to work. Unique_extracted_objects only work for elliptic-shapped apertures
# We get the number of frames from the cube
frame_data = [i for i in range(len(diff_cube))]
# Random colours array
colours = [
(random.uniform(0.5, 1), random.uniform(0.5, 1), random.uniform(0.5, 1))
for i in range(len(unique_extracted_objects))
]
maxVal = 0
minVal = float("inf")
plt.figure(2, figsize=(10, 12))
# Bonus: Show the image with the sources on the same colour than the plots.
if len(diff_cube) == 1:
plt.imshow(diff_cube[0], cmap="gray", vmin=1, vmax=12)
else:
plt.imshow(diff_cube[1], cmap="gray", vmin=1, vmax=12)
plt.colorbar()
for i, extracted_obj in enumerate(unique_extracted_objects):
positions = (extracted_obj[0], extracted_obj[1])
apertures = CircularAperture(positions, r=5.0)
apertures.plot(color=colours[i], linewidth=10.0, lw=2.5, alpha=0.5)
# For every object we are going to calculate the aperture
plt.figure(1, figsize=(20, 12))
for i, extracted_obj in enumerate(unique_extracted_objects):
ap_data = []
# The standard size of each independent figure
# plt.figure(i, figsize=(10, 12))
# For every frame...
for frame in diff_cube:
diff_cube_test = frame.copy()
# The parameters passed in order are x, y, a, b and theta
flux, fluxerr, flag = sep.sum_ellipse(
diff_cube_test,
x=extracted_obj[0],
y=extracted_obj[1],
a=extracted_obj[2],
b=extracted_obj[3],
theta=extracted_obj[4],
)
ap_data.append(flux)
maxVal = np.maximum(maxVal, np.max(ap_data))
minVal = np.minimum(minVal, np.min(ap_data))
# Hard-coded value!!! ALERT!!!
# Plot every curve as a dotted line with the points visible
plt.plot(frame_data, ap_data, "-o", color=colours[i], linewidth=5.0)
plt.ylim((minVal * 1.1, maxVal * 0.9))
# Voila
plt.show()
def _measure(self, img, sources, mask=None):
logger.info('measuring source parameters')
# HACK: issues with numerical precision
# must have pi/2 <= theta <= npi/2
sources[np.abs(np.abs(sources['theta']) - np.pi/2) < 1e-6] = np.pi/2
for p in ['x', 'y', 'a', 'b', 'theta']:
sources = sources[~np.isnan(sources[p])]
# calculate "AUTO" parameters
kronrad, krflag = sep.kron_radius(
img, sources['x'], sources['y'], sources['a'], sources['b'],
sources['theta'], 6.0, mask=mask)
flux, fluxerr, flag = sep.sum_ellipse(
img, sources['x'], sources['y'], sources['a'], sources['b'],
sources['theta'], 2.5*kronrad, subpix=5, mask=mask)
flag |= krflag # combine flags into 'flag'
sources = sources[~np.isnan(flux)]
flux = flux[~np.isnan(flux)]
sources = sources[flux > 0]
flux = flux[flux > 0]
mag_auto = utils.zpt - 2.5*np.log10(flux)
r, flag = sep.flux_radius(
img, sources['x'], sources['y'], 6.*sources['a'], 0.5,
normflux=flux, subpix=5, mask=mask)
sources['mag_auto'] = mag_auto
sources['flux_auto'] = flux
sources['flux_radius'] = r * utils.pixscale
# approximate fwhm
r_squared = sources['a']**2 + sources['b']**2
sources['fwhm'] = 2 * np.sqrt(np.log(2) * r_squared) * utils.pixscale
q = sources['b'] / sources['a']
area = np.pi * q * sources['flux_radius']**2
sources['mu_ave_auto'] = sources['mag_auto'] + 2.5 * np.log10(2*area)
area_arcsec = np.pi * (self.psf_fwhm/2)**2 * utils.pixscale**2
flux, fluxerr, flag = sep.sum_circle(
img, sources['x'], sources['y'], self.psf_fwhm/2,
subpix=5, mask=mask)
flux[flux<=0] = np.nan
mu_0 = utils.zpt - 2.5*np.log10(flux / area_arcsec)
sources['mu_0_aper'] = mu_0
return sources
def test_apertures_all():
"""Test that aperture subpixel sampling works"""
data = np.random.rand(*data_shape)
r = 3.
rtol=1.e-8
for subpix in [0, 1, 5]:
flux_ref, fluxerr_ref, flag_ref = sep.sum_circle(data, x, y, r,
subpix=subpix)
flux, fluxerr, flag = sep.sum_circann(data, x, y, 0., r,
subpix=subpix)
assert_allclose(flux, flux_ref, rtol=rtol)
flux, fluxerr, flag = sep.sum_ellipse(data, x, y, r, r, 0.,
subpix=subpix)
assert_allclose(flux, flux_ref, rtol=rtol)
flux, fluxerr, flag = sep.sum_ellipse(data, x, y, 1., 1., 0., r=r,
subpix=subpix)
assert_allclose(flux, flux_ref, rtol=rtol)
def test_aperture_bkgann_overlapping():
"""Test bkgann functionality in circular & elliptical apertures."""
# If bkgann overlaps aperture exactly, result should be zero
# (with subpix=1)
data = np.random.rand(*data_shape)
r = 5.
f, _, _ = sep.sum_circle(data, x, y, r, bkgann=(0., r), subpix=1)
assert_allclose(f, 0., rtol=0., atol=1.e-13)
f, _, _ = sep.sum_ellipse(data, x, y, 2., 1., np.pi/4., r=r,
bkgann=(0., r), subpix=1)
assert_allclose(f, 0., rtol=0., atol=1.e-13)
def test_aperture_bkgann_ones():
"""Test bkgann functionality with flat data"""
data = np.ones(data_shape)
r=5.
bkgann=(6., 8.)
# On flat data, result should be zero for any bkgann and subpix
f, _, _ = sep.sum_circle(data, x, y, r, bkgann=bkgann)
assert_allclose(f, 0., rtol=0., atol=1.e-13)
f, _, _ = sep.sum_ellipse(data, x, y, 2., 1., np.pi/4., r, bkgann=bkgann)
assert_allclose(f, 0., rtol=0., atol=1.e-13)
def find_flux(tbdat_sub, objects, kronrad, kronflag): flux, fluxerr, flag = sep.sum_ellipse(tbdat_sub, objects['x'], objects['y'], objects['a'], objects['b'], objects['theta'], pho_auto_A = (2.5*kronrad), err = bkg.globalrms, subpix=1) flag |=kronflag #combines all flags r_min = 1.75 #minimum diameter = 3.5 use_circle = kronrad * np.sqrt(a * b) < r_min cflux, cfluxerr, cflag = sep.sum_circle(tbdat_sub, objects['x'][use_circle], objects['y'][use_circle], r_min, subpix=1) flux[use_circle] = cflux fluxerr[use_circle] = cfluxerr flag[use_circle] = cflag r, rflag = sep.flux_radius(data, x, y, 6.0*objects['a'], rmax = 0.5, normflux = flux, subpix =5) sig = 2.0 / (2.35*r) # r from sep.flux_radius() above, with fluxfrac = 0.5 xwin, ywin, wflag = sep.winpos(tbdat_sub, objects['x'], objects['y'], sig) return flux, fluxerr, flag, r, xwin, ywin
def sextractor(im,err=None,mask=None,nsig=5.0,gain=1.0):
# Check byte order, SEP needs little endian
if im.dtype.byteorder == '>':
data = im.byteswap().newbyteorder()
else:
data = im
# Background estimation and subtraction
bkg = sep.Background(data, mask, bw=256, bh=256, fw=3, fh=3)
bkg_image = bkg.back()
data_sub = data-bkg
#data_sub[data>50000]=0.0
# Detect and extract objects
if err is None:
objects = sep.extract(data_sub, nsig, err=bkg.globalrms, mask=mask)
else:
objects = sep.extract(data_sub, nsig, err=err, mask=mask)
# Get mag_auto in 2 steps
kronrad, krflag = sep.kron_radius(data_sub, objects['x'], objects['y'], objects['a'], objects['b'],
objects['theta'], 6.0, mask=mask)
flux, fluxerr, flag = sep.sum_ellipse(data_sub, objects['x'], objects['y'], objects['a'], objects['b'],
objects['theta'], 2.5*kronrad, subpix=1, err=err, mask=mask, gain=gain)
flag |= krflag # combine flags into 'flag'
# Use circular aperture if Kron radius is too small
r_min = 1.75 # minimum diameter = 3.5
use_circle = kronrad * np.sqrt(objects['a'] * objects['b']) < r_min
if np.sum(use_circle)>0:
cflux, cfluxerr, cflag = sep.sum_circle(data_sub, objects['x'][use_circle], objects['y'][use_circle],
r_min, subpix=1, err=err, mask=mask, gain=gain)
flux[use_circle] = cflux
fluxerr[use_circle] = cfluxerr
flag[use_circle] = cflag
mag_auto = -2.5*np.log10(flux)+25.0
magerr_auto = 1.0857*fluxerr/flux
# Make the final catalog
newdt = np.dtype([('kronrad',float),('flux_auto',float),('fluxerr_auto',float),('mag_auto',float),('magerr_auto',float)])
cat = dln.addcatcols(objects,newdt)
cat['flag'] |= flag
cat['kronrad'] = kronrad
cat['flux_auto'] = flux
cat['fluxerr_auto'] = fluxerr
cat['mag_auto'] = mag_auto
cat['magerr_auto'] = magerr_auto
return cat
def _get_flux_auto(self, objs):
flux_auto = np.zeros(objs.size) - 9999.0
fluxerr_auto = np.zeros(objs.size) - 9999.0
flux_radius = np.zeros(objs.size) - 9999.0
kron_radius = np.zeros(objs.size) - 9999.0
w, = np.where((objs['a'] >= 0.0) & (objs['b'] >= 0.0)
& (objs['theta'] >= -np.pi / 2.)
& (objs['theta'] <= np.pi / 2.))
if w.size > 0:
kron_radius[w], krflag = sep.kron_radius(
self.image,
objs['x'][w],
objs['y'][w],
objs['a'][w],
objs['b'][w],
objs['theta'][w],
6.0,
)
objs['flag'][w] |= krflag
aper_rad = 2.5 * kron_radius
flux_auto[w], fluxerr_auto[w], flag_auto = \
sep.sum_ellipse(
self.image,
objs['x'][w],
objs['y'][w],
objs['a'][w],
objs['b'][w],
objs['theta'][w],
aper_rad[w],
subpix=1,
)
objs['flag'][w] |= flag_auto
flux_radius[w], frflag = sep.flux_radius(
self.image,
objs['x'][w],
objs['y'][w],
6. * objs['a'][w],
PHOT_FLUXFRAC,
normflux=flux_auto[w],
subpix=5,
)
objs['flag'][w] |= frflag # combine flags into 'flag'
return flux_auto, fluxerr_auto, flux_radius, kron_radius
def make_sep_catalog(data,
header,
options,
mask=None,
min_sep=10.,
do_bgsub=False):
try:
bkg = sep.Background(data, mask, bw=32, bh=32, fw=3, fh=3)
except ValueError:
data = data.byteswap().newbyteorder()
bkg = sep.Background(data, mask, bw=32, bh=32, fw=3, fh=3)
if do_bgsub:
error = np.sqrt(data)
data_bgsub = data - bkg
else:
error = bkg.globalrms
data_bgsub = data
sources = sep.extract(data_bgsub, err=error, mask=mask, **options['sep'])
dists = ((sources['x'] - sources['x'][:, np.newaxis])**2 +
(sources['y'] - sources['y'][:, np.newaxis])**2)**0.5
closest = np.partition(dists, 1)[:, 1]
sources = sources[closest > min_sep]
t = table.Table(sources)
kronrad, krflag = sep.kron_radius(data_bgsub, sources['x'], sources['y'],
sources['a'], sources['b'],
sources['theta'], 6.0)
flux, fluxerr, flag = sep.sum_ellipse(data_bgsub,
sources['x'],
sources['y'],
sources['a'],
sources['b'],
np.pi / 2.0,
2.5 * kronrad,
subpix=1,
err=error)
t['mag'] = -2.5 * np.log10(flux)
t['magerr'] = np.log(10) / 2.5 * fluxerr / flux
t['ra'], t['dec'] = WCS(header).all_pix2world(t['x'], t['y'], 0)
t = t['x', 'y', 'mag', 'magerr', 'ra', 'dec']
return t
def extract(data):
bkg = sep.Background(data, bw=64, bh=64, fw=3, fh=3)
bkg.subfrom(data)
objs = sep.extract(data, 1.5*bkg.globalrms)
flux, fluxerr, flag = sep.sum_circle(data, objs['x'], objs['y'], 5.,
err=bkg.globalrms)
kr, flag = sep.kron_radius(data, objs['x'], objs['y'], objs['a'],
objs['b'], objs['theta'], 6.0)
eflux, efluxerr, eflag = sep.sum_ellipse(data, objs['x'], objs['y'],
objs['a'], objs['b'],
objs['theta'], r=2.5 * kr,
err=bkg.globalrms, subpix=1)
retstr = ""
for i in range(len(objs['x'])):
retstr = retstr+(str(objs['x'][i])+"\t"+str(objs['y'][i])+"\t"+str(flux[i])+"\t"+str(fluxerr[i])+"\t"+str(kr[i])+"\t"+str(eflux[i])+"\t"+str(efluxerr[i])+"\t"+str(flag[i])+"\n")
return retstr
def test_aperture_bkgann_ones():
"""Test bkgann functionality with flat data"""
data = np.ones(data_shape)
r=5.
bkgann=(6., 8.)
# On flat data, result should be zero for any bkgann and subpix
f, fe, _ = sep.sum_circle(data, x, y, r, bkgann=bkgann, gain=1.)
assert_allclose(f, 0., rtol=0., atol=1.e-13)
# for all ones data and no error array, error should be close to
# sqrt(Npix_aper + Npix_ann * (Npix_aper**2 / Npix_ann**2))
aper_area = np.pi * r**2
bkg_area = np.pi * (bkgann[1]**2 - bkgann[0]**2)
expected_error = np.sqrt(aper_area + bkg_area * (aper_area/bkg_area)**2)
assert_allclose(fe, expected_error, rtol=0.1)
f, _, _ = sep.sum_ellipse(data, x, y, 2., 1., np.pi/4., r, bkgann=bkgann)
assert_allclose(f, 0., rtol=0., atol=1.e-13)
def findSpot(data, sigma):
image=data
#m, s = np.mean(image), np.std(image)
bkg = sep.Background(image, bw=32, bh=32, fw=3, fh=3)
objs = sep.extract(image-bkg, sigma, err=bkg.globalrms)
aper_radius=3
# Calculate the Kron Radius
kronrad, krflag = sep.kron_radius(image, objs['x'], objs['y'], \
objs['a'], objs['b'], objs['theta'], aper_radius)
r_min = 3
use_circle = kronrad * np.sqrt(objs['a'] * objs['b'])
cinx=np.where(use_circle <= r_min)
einx=np.where(use_circle > r_min)
# Calculate the equivalent of FLUX_AUTO
flux, fluxerr, flag = sep.sum_ellipse(image, objs['x'][einx], objs['y'][einx], \
objs['a'][einx], objs['b'][einx], objs['theta'][einx], 2.5*kronrad[einx],subpix=1)
cflux, cfluxerr, cflag = sep.sum_circle(image, objs['x'][cinx], objs['y'][cinx],
objs['a'][cinx], subpix=1)
# Adding half pixel to measured coordinate.
objs['x'] = objs['x']+0.5
objs['y'] = objs['y']+0.5
objs['flux'][einx]=flux
objs['flux'][cinx]=cflux
r, flag = sep.flux_radius(image, objs['x'], objs['y'], \
6*objs['a'], 0.3,normflux=objs['flux'], subpix=5)
flag |= krflag
objs=rfn.append_fields(objs, 'r', data=r, usemask=False)
objects=objs[:]
return objects
def aperture_photometry(data, x, y, r, r_in, r_out,
elipse = False, abtheta = None,
rms = None,
*args, **kwargs):
'''
Do the aperture photometry with local sky subtraction.
Parameters:
data : ~numpy.ndarray~
2D image data.
x, y : list of list of float
The list containing the pairs (x,y) of the objects.
r : float
The radius of the circular aperture to do the sum.
r_in : float
The internal radius of the sky annulus.
r_out : float
The external radius of the sky annulus.
elipse : bool
Tell the program if you want to do the photometry with eliptical
aperture. If True, you have to pass the 'abtheta' argument, giving
the elipse properties.
**The kwargs will be passed integrally to the sep functions.
Returns:
flux, fluxerr, flags : ~numpy.ndarray~
The sum of the aperture, with annulus sky subtraction, and its error.
'''
data = _fix_data(data)
if elipse:
if abtheta is None:
raise ValueError("You must give the 'abtheta' argument if you want elipse photometry.")
a, b, theta = _extract_abtheta(abtheta)
return sep.sum_ellipse(data, x, y, a, b, theta, r, err=rms, bkgann=(r_in, r_out), **kwargs)
else:
return sep.sum_circle(data, x, y, r, err=rms, bkgann=(r_in, r_out), **kwargs)
def do_stage(self, image):
try:
# Set the number of source pixels to be 5% of the total. This keeps us safe from
# satellites and airplanes.
sep.set_extract_pixstack(int(image.nx * image.ny * 0.05))
data = image.data.copy()
error = (np.abs(data) + image.readnoise**2.0)**0.5
mask = image.bpm > 0
# Fits can be backwards byte order, so fix that if need be and subtract
# the background
try:
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
except ValueError:
data = data.byteswap(True).newbyteorder()
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
bkg.subfrom(data)
# Do an initial source detection
# TODO: Add back in masking after we are sure SEP works
sources = sep.extract(data,
self.threshold,
minarea=self.min_area,
err=error,
deblend_cont=0.005)
# Convert the detections into a table
sources = Table(sources)
# We remove anything with a detection flag >= 8
# This includes memory overflows and objects that are too close the edge
sources = sources[sources['flag'] < 8]
sources = array_utils.prune_nans_from_table(sources)
# Calculate the ellipticity
sources['ellipticity'] = 1.0 - (sources['b'] / sources['a'])
# Fix any value of theta that are invalid due to floating point rounding
# -pi / 2 < theta < pi / 2
sources['theta'][sources['theta'] > (np.pi / 2.0)] -= np.pi
sources['theta'][sources['theta'] < (-np.pi / 2.0)] += np.pi
# Calculate the kron radius
kronrad, krflag = sep.kron_radius(data, sources['x'], sources['y'],
sources['a'], sources['b'],
sources['theta'], 6.0)
sources['flag'] |= krflag
sources['kronrad'] = kronrad
# Calcuate the equivilent of flux_auto
flux, fluxerr, flag = sep.sum_ellipse(data,
sources['x'],
sources['y'],
sources['a'],
sources['b'],
np.pi / 2.0,
2.5 * kronrad,
subpix=1,
err=error)
sources['flux'] = flux
sources['fluxerr'] = fluxerr
sources['flag'] |= flag
# Do circular aperture photometry for diameters of 1" to 6"
for diameter in [1, 2, 3, 4, 5, 6]:
flux, fluxerr, flag = sep.sum_circle(data,
sources['x'],
sources['y'],
diameter / 2.0 /
image.pixel_scale,
gain=1.0,
err=error)
sources['fluxaper{0}'.format(diameter)] = flux
sources['fluxerr{0}'.format(diameter)] = fluxerr
sources['flag'] |= flag
# Calculate the FWHMs of the stars:
fwhm = 2.0 * (np.log(2) *
(sources['a']**2.0 + sources['b']**2.0))**0.5
sources['fwhm'] = fwhm
# Cut individual bright pixels. Often cosmic rays
sources = sources[fwhm > 1.0]
# Measure the flux profile
flux_radii, flag = sep.flux_radius(data,
sources['x'],
sources['y'],
6.0 * sources['a'],
[0.25, 0.5, 0.75],
normflux=sources['flux'],
subpix=5)
sources['flag'] |= flag
sources['fluxrad25'] = flux_radii[:, 0]
sources['fluxrad50'] = flux_radii[:, 1]
sources['fluxrad75'] = flux_radii[:, 2]
# Calculate the windowed positions
sig = 2.0 / 2.35 * sources['fluxrad50']
xwin, ywin, flag = sep.winpos(data, sources['x'], sources['y'],
sig)
sources['flag'] |= flag
sources['xwin'] = xwin
sources['ywin'] = ywin
# Calculate the average background at each source
bkgflux, fluxerr, flag = sep.sum_ellipse(bkg.back(),
sources['x'],
sources['y'],
sources['a'],
sources['b'],
np.pi / 2.0,
2.5 * sources['kronrad'],
subpix=1)
# masksum, fluxerr, flag = sep.sum_ellipse(mask, sources['x'], sources['y'],
# sources['a'], sources['b'], np.pi / 2.0,
# 2.5 * kronrad, subpix=1)
background_area = (
2.5 * sources['kronrad']
)**2.0 * sources['a'] * sources['b'] * np.pi # - masksum
sources['background'] = bkgflux
sources['background'][background_area > 0] /= background_area[
background_area > 0]
# Update the catalog to match fits convention instead of python array convention
sources['x'] += 1.0
sources['y'] += 1.0
sources['xpeak'] += 1
sources['ypeak'] += 1
sources['xwin'] += 1.0
sources['ywin'] += 1.0
sources['theta'] = np.degrees(sources['theta'])
catalog = sources['x', 'y', 'xwin', 'ywin', 'xpeak', 'ypeak',
'flux', 'fluxerr', 'peak', 'fluxaper1',
'fluxerr1', 'fluxaper2', 'fluxerr2', 'fluxaper3',
'fluxerr3', 'fluxaper4', 'fluxerr4', 'fluxaper5',
'fluxerr5', 'fluxaper6', 'fluxerr6',
'background', 'fwhm', 'a', 'b', 'theta',
'kronrad', 'ellipticity', 'fluxrad25',
'fluxrad50', 'fluxrad75', 'x2', 'y2', 'xy',
'flag']
# Add the units and description to the catalogs
catalog['x'].unit = 'pixel'
catalog['x'].description = 'X coordinate of the object'
catalog['y'].unit = 'pixel'
catalog['y'].description = 'Y coordinate of the object'
catalog['xwin'].unit = 'pixel'
catalog['xwin'].description = 'Windowed X coordinate of the object'
catalog['ywin'].unit = 'pixel'
catalog['ywin'].description = 'Windowed Y coordinate of the object'
catalog['xpeak'].unit = 'pixel'
catalog['xpeak'].description = 'X coordinate of the peak'
catalog['ypeak'].unit = 'pixel'
catalog['ypeak'].description = 'Windowed Y coordinate of the peak'
catalog['flux'].unit = 'count'
catalog[
'flux'].description = 'Flux within a Kron-like elliptical aperture'
catalog['fluxerr'].unit = 'count'
catalog[
'fluxerr'].description = 'Error on the flux within Kron aperture'
catalog['peak'].unit = 'count'
catalog['peak'].description = 'Peak flux (flux at xpeak, ypeak)'
for diameter in [1, 2, 3, 4, 5, 6]:
catalog['fluxaper{0}'.format(diameter)].unit = 'count'
catalog['fluxaper{0}'.format(
diameter
)].description = 'Flux from fixed circular aperture: {0}" diameter'.format(
diameter)
catalog['fluxerr{0}'.format(diameter)].unit = 'count'
catalog['fluxerr{0}'.format(
diameter
)].description = 'Error on Flux from circular aperture: {0}"'.format(
diameter)
catalog['background'].unit = 'count'
catalog[
'background'].description = 'Average background value in the aperture'
catalog['fwhm'].unit = 'pixel'
catalog['fwhm'].description = 'FWHM of the object'
catalog['a'].unit = 'pixel'
catalog['a'].description = 'Semi-major axis of the object'
catalog['b'].unit = 'pixel'
catalog['b'].description = 'Semi-minor axis of the object'
catalog['theta'].unit = 'degree'
catalog['theta'].description = 'Position angle of the object'
catalog['kronrad'].unit = 'pixel'
catalog['kronrad'].description = 'Kron radius used for extraction'
catalog['ellipticity'].description = 'Ellipticity'
catalog['fluxrad25'].unit = 'pixel'
catalog[
'fluxrad25'].description = 'Radius containing 25% of the flux'
catalog['fluxrad50'].unit = 'pixel'
catalog[
'fluxrad50'].description = 'Radius containing 50% of the flux'
catalog['fluxrad75'].unit = 'pixel'
catalog[
'fluxrad75'].description = 'Radius containing 75% of the flux'
catalog['x2'].unit = 'pixel^2'
catalog[
'x2'].description = 'Variance on X coordinate of the object'
catalog['y2'].unit = 'pixel^2'
catalog[
'y2'].description = 'Variance on Y coordinate of the object'
catalog['xy'].unit = 'pixel^2'
catalog['xy'].description = 'XY covariance of the object'
catalog[
'flag'].description = 'Bit mask of extraction/photometry flags'
catalog.sort('flux')
catalog.reverse()
# Save some background statistics in the header
mean_background = stats.sigma_clipped_mean(bkg.back(), 5.0)
image.header['L1MEAN'] = (
mean_background,
'[counts] Sigma clipped mean of frame background')
median_background = np.median(bkg.back())
image.header['L1MEDIAN'] = (median_background,
'[counts] Median of frame background')
std_background = stats.robust_standard_deviation(bkg.back())
image.header['L1SIGMA'] = (
std_background, '[counts] Robust std dev of frame background')
# Save some image statistics to the header
good_objects = catalog['flag'] == 0
for quantity in ['fwhm', 'ellipticity', 'theta']:
good_objects = np.logical_and(
good_objects, np.logical_not(np.isnan(catalog[quantity])))
if good_objects.sum() == 0:
image.header['L1FWHM'] = ('NaN',
'[arcsec] Frame FWHM in arcsec')
image.header['L1ELLIP'] = ('NaN',
'Mean image ellipticity (1-B/A)')
image.header['L1ELLIPA'] = (
'NaN', '[deg] PA of mean image ellipticity')
else:
seeing = np.median(
catalog['fwhm'][good_objects]) * image.pixel_scale
image.header['L1FWHM'] = (seeing,
'[arcsec] Frame FWHM in arcsec')
mean_ellipticity = stats.sigma_clipped_mean(
catalog['ellipticity'][good_objects], 3.0)
image.header['L1ELLIP'] = (mean_ellipticity,
'Mean image ellipticity (1-B/A)')
mean_position_angle = stats.sigma_clipped_mean(
catalog['theta'][good_objects], 3.0)
image.header['L1ELLIPA'] = (
mean_position_angle, '[deg] PA of mean image ellipticity')
logging_tags = {
key: float(image.header[key])
for key in [
'L1MEAN', 'L1MEDIAN', 'L1SIGMA', 'L1FWHM', 'L1ELLIP',
'L1ELLIPA'
]
}
logger.info('Extracted sources',
image=image,
extra_tags=logging_tags)
# adding catalog (a data table) to the appropriate images attribute.
image.data_tables['catalog'] = DataTable(data_table=catalog,
name='CAT')
except Exception:
logger.error(logs.format_exception(), image=image)
return image
def run(self):
""" Runs the calibrating algorithm. The calibrated data is
returned in self.dataout
"""
### Preparation
binning = self.datain.getheadval('XBIN')
### Run Source Extractor
# Make sure input data exists as file
if not os.path.exists(self.datain.filename):
self.datain.save()
'''
# Make catalog filename
catfilename = self.datain.filenamebegin
if catfilename[-1] in '._-': catfilename += 'sex_cat.fits'
else: catfilename += '.sex_cat.fits'
# Make background filename (may not be used - see below)
bkgdfilename = self.datain.filenamebegin
if bkgdfilename[-1] in '._-': bkgdfilename += 'SxBkgd.fits'
else: bkgdfilename += '_SxBkgd.fits'
self.log.debug('Sextractor catalog filename = %s' % catfilename)
'''
#Open data out of fits file for use in SEP
image = self.datain.image
#Set values for variables used later
#These variables are used for the background analysis. bw and bh I found just testing various numbers
maskthresh = 0.0
bw, bh = 10, 10
fw, fh = 3, 3
fthresh = 0.0
#Create the background image and it's error
bkg = sep.Background(
image,
maskthresh=maskthresh,
bw=bw,
bh=bh,
fw=fw,
fh=fh,
fthresh=fthresh) #have sep determine the background of the image
bkg_image = bkg.back()
bkg_rms = bkg.rms()
#Subtract the background from the image
image_sub = image - bkg_image
imsubmed = np.nanmedian(image_sub)
imsubmad = mad_std(image_sub)
#Create variables that are used during source Extraction
extract_thresh = 5
extract_err = bkg_rms
#Extract sources from the subtracted image
objects = sep.extract(image_sub, extract_thresh, err=extract_err)
#Define variables used later during flux calculation
sum_c = np.zeroes(len(objects))
sum_c_err = np.zeroes(len(objects))
sum_c_flags = np.zeroes(len(objects))
ratio = np.zeroes(len(objects))
rmax = np.zeroes(len(objects))
dx = np.zeros(len(objects))
dy = np.zeros(len(objects))
#Do basic uncalibrated measurments of flux for use in step astrometry.
#First we calculate flux using Ellipses. In order to do this we need to calculate the Kron Radius
#For the ellipses Extract identified using the ellipse parameters it gives
#R is equal to 6 as that is the default used in Source Extractor
kronrad, krflag = sep.kron_radius(image_sub,
objects['x'],
objects['y'],
objects['a'],
objects['b'],
objects['theta'],
r=6)
#Using this Kron radius we calculate the flux, this is equivallent to FLUX_AUTO in SExtractor
flux_elip, fluxerr_elip, flag = sep.sum_ellipse(image_sub,
objects['x'],
objects['y'],
objects['a'],
objects['b'],
objects['theta'],
2.5 * kronrad,
err=bkg_rms,
subpix=1)
#Then we calculate it using Circular Apetures, this will be used to remove sources that are too elipitical
flux_circ, fluxerr_circ, flag = sep.sum_circle(image_sub,
objects['x'],
objects['y'],
r=2.5,
err=bkg_rms,
subpix=1)
### Extract catalog from source extractor and clean up dataset
# Use catalog from sourse extrator (test.cat)
#seo_catalog = astropy.table.Table.read(catfilename, format="fits", hdu='LDAC_OBJECTS')
seo_Mag = -2.5 * np.log10(flux_elip)
seo_MagErr = (2.5 / np.log(10) * (fluxerr_elip / flux_elip))
# Select only the stars in the image: circular image and S/N > 10
elongation = (flux_circ - flux_elip) < 250
seo_SN = ((flux_elip / fluxerr_elip) > 10)
seo_SN = (seo_SN) & (elongation) & (
(flux_elip / fluxerr_elip) < 1000) & (fluxerr_elip != 0)
self.log.debug('Selected %d stars from Source Extrator catalog' %
np.count_nonzero(seo_SN))
### Query and extract data from Guide Star Catalog
# Get RA / Dec
'''
ra_center = self.datain.getheadval('RA' ).split(':')
dec_center = self.datain.getheadval('DEC').split(':')
ra_cent = ' '.join([str(s) for s in ra_center])
dec_cent = ' '.join([str(s) for s in dec_center])
center_coordinates = SkyCoord(ra_cent + ' ' + dec_cent, unit=(u.hourangle, u.deg) )
self.log.debug('Using RA/Dec = %s / %s' % (center_coordinates.ra, center_coordinates.dec) )
# Querry guide star catalog2 with center coordinates
gsc2_query = 'http://gsss.stsci.edu/webservices/vo/CatalogSearch.aspx?'
gsc2_query += 'RA='+str(center_coordinates.ra.value)
gsc2_query += '&DEC='+str(center_coordinates.dec.value)
gsc2_query += '&DSN=+&FORMAT=CSV&CAT=GSC241&SR=0.5&'
self.log.debug('Running URL = %s' % gsc2_query)
gsc2_result = requests.get(gsc2_query)
# Get data from result
filter_map = self.getarg('filtermap').split('|')
filter_name = filter_tel = self.datain.getheadval('FILTER')
for fil in filter_map:
entry = fil.split('=')
if entry[0] == filter_tel:
try:
filter_name = entry[1]
except:
self.log.error("Badly formatted filter mapping. No '=' after %s"
% filter_tel)
query_table = astropy.io.ascii.read(gsc2_result.text)
table_filter = 'SDSS'+filter_name+'Mag'
table_filter_err = 'SDSS'+filter_name+'MagErr'
GSC_RA = query_table['ra'][(query_table[table_filter]<22) & (query_table[table_filter]>0)]
GSC_DEC = query_table['dec'][(query_table[table_filter]<22) & (query_table[table_filter]>0)]
GSC_Mag = query_table[table_filter][(query_table[table_filter]<22) & (query_table[table_filter]>0)]
GSC_MagErr = query_table[table_filter_err][(query_table[table_filter]<22) & (query_table[table_filter]>0)]
self.log.debug('Received %d entries from Guide Star Catalog' % len(GSC_RA))
### Mach Guide Star Catalog data with data from Source Extractor
# Do the matching
seo_radec = SkyCoord(ra=seo_catalog['ALPHA_J2000'], dec=seo_catalog['DELTA_J2000'])
GSC_radec = SkyCoord(ra=GSC_RA*u.deg, dec=GSC_DEC*u.deg)
idx, d2d, d3d = GSC_radec.match_to_catalog_sky(seo_radec[seo_SN])
# only select objects less than 0.025 away in distance, get distance value
dist_value = 1*0.76*binning/3600. #Maximum distance is 1 pixel
mask = d2d.value<dist_value
if(np.sum(mask) < 2):
self.log.warn('Only %d sources match between image and guide star catalog, fit may not work' %
np.sum(mask) )
self.log.debug('Distance_Value = %f, Min(distances) = %f, Mask length = %d' %
( dist_value, np.min(d2d.value), np.sum(mask) ) )
### Calculate the fit correction between the guide star and the extracted values
# Make lambda function to be minimized
# The fit finds m_ml and b_ml where
# seo_Mag = b_ml + m_ml * GSC_Mag
nll = lambda *args: -residual(*args)
# Get errors
eps_data = np.sqrt(GSC_MagErr**2+seo_MagErr[seo_SN][idx]**2)
# Make estimate for intercept to give as initial guess
b_ml0 = np.median(seo_Mag[seo_SN][idx][mask]-GSC_Mag[mask])
self.log.debug('Offset guess is %f mag' % b_ml0)
# Calculate distance from that guess and get StdDev of distances
guessdistances = np.abs( b_ml0 - ( seo_Mag[seo_SN][idx] - GSC_Mag ) )
guessdistmed = np.median(guessdistances[mask])
# Update mask to ignore values with large STDEVS
mask = np.logical_and( d2d.value < dist_value, guessdistances < 5 * guessdistmed )
self.log.debug('Median of distance to guess = %f, Mask length = %d' %
( guessdistmed, np.sum(mask) ) )
# Solve linear equation
result = scipy.optimize.minimize(nll, [1, b_ml0],
args=(GSC_Mag[mask],
seo_Mag[seo_SN][idx][mask],
eps_data[mask]))
m_ml, b_ml = result["x"]
self.log.info('Fitted offset is %f mag, fitted slope is %f' % (b_ml, m_ml) )
b_ml_corr = b_ml + (m_ml-1) * np.median(GSC_Mag[mask])
self.log.info('Corrected offset is %f mag' % b_ml_corr)
'''
### Make table with all data from source extractor
# Collect data columns
cols = []
num = np.arange(1, len(objects['x']) + 1)
cols.append(fits.Column(name='ID', format='D', array=num))
cols.append(
fits.Column(name='X',
format='D',
array=objects['x'][seo_SN],
unit='pixel'))
cols.append(
fits.Column(name='Y',
format='D',
array=objects['y'][seo_SN],
unit='pixel'))
cols.append(
fits.Column(name='Uncalibrated Magnitude',
format='D',
array=seo_Mag,
unit='magnitude'))
cols.append(
fits.Column(name='Uncalibrated Magnitude_Err',
format='D',
array=seo_MagErr,
unit='magnitude'))
# Make table
c = fits.ColDefs(cols)
sources_table = fits.BinTableHDU.from_columns(c)
'''
### Make table with data which was fit
# Collect data columns
cols = []
cols.append(fits.Column(name='RA', format='D', array=GSC_RA[mask],
unit='deg'))
cols.append(fits.Column(name='Dec', format='D', array=GSC_DEC[mask],
unit='deg'))
cols.append(fits.Column(name='Diff_Deg', format='D', array=d2d[mask],
unit='deg'))
cols.append(fits.Column(name='GSC_Mag', format='D',
array=GSC_Mag[mask], unit='magnitude'))
cols.append(fits.Column(name='Img_Mag', format='D',
array=seo_Mag[seo_SN][idx][mask],
unit='magnitude'))
cols.append(fits.Column(name='Error', format='D', array=eps_data[mask],
unit='magnitude'))
# Make table
c = fits.ColDefs(cols)
fitdata_table = fits.BinTableHDU.from_columns(c)
'''
### Make output data
# Copy data from datain
self.dataout = self.datain
'''
# Add Photometric Zero point magnitude
self.dataout.setheadval('PHTZPRAW', -b_ml_corr, 'Photometric zeropoint for RAW data')
self.dataout.setheadval('PTZRAWER', 0.0, 'Uncertainty of the RAW photometric zeropoint')
self.dataout.setheadval('PHOTZP', 8.9, 'Photometric zeropoint MAG=-2.5*log(data)+PHOTZP')
self.dataout.setheadval('BUNIT', 'Jy/pixel', 'Units for the data')
'''
# Scale the image using calculated b_ml_corr
#image_background = fits.open(bkgdfilename)[0].data
#bzero = np.nanpercentile(self.dataout.image,self.getarg('zeropercent'))
#bzero = image_background
#-- Alternative bzero idea:
#-mask = image_array < np.percentile(image,90)
#-bzero = np.median(image_array[mask])
#bscale = 3631. * 10 ** (b_ml_corr/2.5)
#self.dataout.image = bscale * (self.dataout.image - bzero)
# Add sources and fitdata table
self.dataout.tableset(sources_table.data, 'Sources',
sources_table.header)
#self.dataout.tableset(fitdata_table.data,'Fit Data',fitdata_table.header)
'''
### If requested make a plot of the fit and save as png
if self.getarg('fitplot'):
# Set up plot
plt.figure(figsize=(10,7))
# Plot 5sigma error range
gmin = min(GSC_Mag[mask])
gmax = max(GSC_Mag[mask])
plt.fill([gmin,gmin,gmax,gmax],[gmin+b_ml0-guessdistmed, gmin+b_ml0+guessdistmed,
gmax+b_ml0+guessdistmed, gmax+b_ml0-guessdistmed],'c')
# Plot fits
plt.plot(GSC_Mag[mask],m_ml*GSC_Mag[mask]+b_ml)
plt.plot(GSC_Mag[mask],GSC_Mag[mask]+b_ml0)
# Plot the datapoints
plt.errorbar(GSC_Mag[d2d.value<dist_value],seo_Mag[seo_SN][idx][d2d.value<dist_value],
yerr=np.sqrt(eps_data[d2d.value<dist_value]**2),fmt='o',linestyle='none')
plt.errorbar(GSC_Mag[mask],seo_Mag[seo_SN][idx][mask],
yerr=np.sqrt(eps_data[mask]**2),fmt='o',linestyle='none')
#plt.plot(GSC_Mag[d2d.value<dist_value],m_ml*GSC_Mag[d2d.value<dist_value]+zeropoint_fit[1])
plt.legend(['LM-fit','Fit-Guess','GuessDistMed Range','d<distval Data','Good Data'])
plt.ylabel('Source extrator magnitude')
plt.xlabel('Star catalog magnitude')
plt.title('Calibration Fit for file\n' + os.path.split(self.dataout.filename)[1])
# Plot the fit
# Axis and labels
# Save the image
pngname = self.dataout.filenamebegin + 'FCALplot.png'
plt.savefig(pngname)
self.log.debug('Saved fit plot under %s' % pngname)
'''
### If requested make a text file with the sources list
if self.getarg('sourcetable'):
# Save region file
filename = self.dataout.filenamebegin + 'FCALsources.reg'
with open(filename, 'w+') as f:
f.write("# Region file format: DS9 version 4.1\n")
f.write(
"""global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1 image\n"""
)
for i in range(len(seo_catalog['x'][seo_SN])):
f.write("circle(%.7f,%.7f,0.005) # text={%i}\n" %
(seo_catalog['x'][seo_SN][i],
seo_catalog['y'][seo_SN][i], num[i]))
# Save the table
txtname = self.dataout.filenamebegin + 'FCALsources.txt'
ascii.write(self.dataout.tableget('Sources'),
txtname,
format=self.getarg('sourcetableformat'))
self.log.debug('Saved sources table under %s' % txtname)
def aperture_photometry(img: Union[ndarray, MaskedArray], sources: ndarray,
background: Optional[Union[ndarray,
MaskedArray]] = None,
background_rms: Optional[Union[ndarray,
MaskedArray]] = None,
texp: float = 1,
gain: Union[float, ndarray, MaskedArray] = 1,
sat_level: float = 63000,
a: Optional[float] = None, b: Optional[float] = None,
theta: Optional[float] = 0,
a_in: Optional[float] = None,
a_out: Optional[float] = None,
b_out: Optional[float] = None,
theta_out: Optional[float] = None,
k: float = 0,
k_in: Optional[float] = None,
k_out: Optional[float] = None,
radius: float = 6,
fix_aper: bool = False,
fix_ell: bool = True,
fix_rot: bool = True,
apcorr_tol: float = 0.0001) -> ndarray:
"""
Do automatic or fixed aperture photometry
:param img: input 2D image array
:param sources: record array of sources extracted with
:func:`skylib.extraction.extract_sources`; should contain at least "x"
and "y" columns
:param background: optional sky background map; if omitted, extract
background from the annulus around the aperture, see `a_in` below
:param background_rms: optional sky background RMS map; if omitted,
calculate RMS over the annulus around the aperture
:param texp: exposure time in seconds
:param gain: electrons to data units conversion factor; used to estimate
photometric errors; for variable-gain images (e.g. mosaics), must be
an array of the same shape as the input data
:param sat_level: saturation level in ADUs; used to select only
non-saturated stars for adaptive aperture photometry and aperture
correction
:param a: fixed aperture radius or semi-major axis in pixels; default: use
automatic photometry with a = a_iso*k, where a_iso is the isophotal
semi-major axis
:param b: semi-minor axis in pixels when using a fixed aperture; default:
same as `a`
:param theta: rotation angle of semi-major axis in degrees CCW when using
a fixed aperture and `b` != `a`; default: 0
:param a_in: inner annulus radius or semi-major axis in pixels; used
to estimate the background if `background` or `background_rms` are not
provided, ignored otherwise; default: `a`*`k_in`
:param a_out: outer annulus radius or semi-major axis in pixels; default:
`a`*`k_out`
:param b_out: outer annulus semi-minor axis in pixels; default: `b`*`k_out`
:param theta_out: annulus orientation in degrees CCW; default: same
as `theta`
:param k: automatic aperture radius in units of isophotal radius; 0 means
find the optimal radius based on SNR; default: 0
:param k_in: inner annulus radius in units of aperture radius (fixed
aperture, i.e. `a` is provided) or isophotal radius (adaptive aperture);
default: 1.5*`k` or 3.75 if `k` is undefined and `a` = None
:param k_out: outer annulus radius in units of aperture radius (fixed
aperture) or isophotal radius (adaptive aperture); default: 2*`k` or
5 if `k` is undefined and `a` = None
:param radius: isophotal analysis radius in pixels used to compute automatic
aperture if ellipse parameters (a,b,theta) are missing
:param fix_aper: use the same aperture radius for all sources when doing
automatic photometry; calculated as flux-weighted median of aperture
sizes based on isophotal parameters
:param fix_ell: use the same major to minor aperture axis ratio for all
sources during automatic photometry; calculated as flux-weighted median
of all ellipticities
:param fix_rot: use the same aperture position angle for all sources during
automatic photometry; calculated as flux-weighted median
of all orientations
:param apcorr_tol: growth curve stopping tolerance for aperture correction;
0 = disable aperture correction
:return: record array containing the input sources, with the following
fields added or updated: "flux", "flux_err", "mag", "mag_err", "aper_a",
"aper_b", "aper_theta", "aper_a_in", "aper_a_out", "aper_b_out",
"aper_theta_out", "aper_area", "background_area", "background",
"background_rms", "phot_flag"
"""
if not len(sources):
return array([])
img = sep_compatible(img)
texp = float(texp)
if isscalar(gain):
gain = float(gain)
k = float(k)
if k <= 0.1:
k = 0 # temporary fix for k = 0 not being allowed in AgA
if k_in:
k_in = float(k_in)
if k_out:
k_out = float(k_out)
x, y = sources['x'] - 1, sources['y'] - 1
area_img = ones(img.shape, dtype=int32)
if isinstance(img, MaskedArray):
mask = img.mask
img = img.data
else:
mask = None
have_background = background is not None and background_rms is not None
if have_background:
background = sep_compatible(background)
if isinstance(background, MaskedArray):
if mask is None:
mask = background.mask
else:
mask |= background.mask
background = background.data
background_rms = sep_compatible(background_rms)
if isinstance(background_rms, MaskedArray):
if mask is None:
mask = background_rms.mask
else:
mask |= background_rms.mask
background_rms = background_rms.data
# Will need this to fill the newly added source table columns
z = zeros(len(sources), float)
fixed_aper = bool(a)
if fixed_aper:
# Use the same fixed aperture and annulus parameters for all sources
a = float(a)
if b:
b = float(b)
else:
b = a
if theta:
theta = float(theta % 180)*pi/180
if theta > pi/2:
theta -= pi
else:
theta = 0
if not have_background:
if theta_out:
theta_out = float(theta_out % 180)*pi/180
if theta_out > pi/2:
theta_out -= pi
elif theta_out != 0:
theta_out = theta
if a_in:
a_in = float(a_in)
else:
a_in = a*k_in if k_in else a*1.5*k if k else a*3.75
if a_out:
a_out = float(a_out)
else:
a_out = a*k_out if k_out else a*2*k if k else a*5
if b_out:
b_out = float(b_out)
else:
b_out = a_out*b/a
else:
# Use automatic apertures derived from ellipse axes; will need image
# with background subtracted
if background is None:
# Estimate background on the fly
tmp_back, tmp_rms = estimate_background(img, size=64)
else:
tmp_back, tmp_rms = background, background_rms
img_back = img - tmp_back
for name in ['a', 'b', 'theta', 'flux']:
if name not in sources.dtype.names:
sources = append_fields(sources, name, z, usemask=False)
a, b, theta = sources['a'], sources['b'], sources['theta']
flux = sources['flux']
bad = (a <= 0) | (b <= 0) | (flux <= 0)
if bad.any():
# Do isophotal analysis to compute ellipse parameters if missing
yy, xx = indices(img.shape)
for i in bad.nonzero()[0]:
ap = (xx - sources[i]['x'])**2 + (yy - sources[i]['y'])**2 <= \
radius**2
if ap.any():
yi, xi = ap.nonzero()
ap_data = img_back[ap].astype(float)
f = ap_data.sum()
if f > 0:
cx = (xi*ap_data).sum()/f
cy = (yi*ap_data).sum()/f
x2 = (xi**2*ap_data).sum()/f - cx**2
y2 = (yi**2*ap_data).sum()/f - cy**2
xy = (xi*yi*ap_data).sum()/f - cx*cy
else:
cx, cy = xi.mean(), yi.mean()
x2 = (xi**2).mean() - cx**2
y2 = (yi**2).mean() - cy**2
xy = (xi*yi).mean() - cx*cy
if x2 == y2:
thetai = 0
else:
thetai = arctan(2*xy/(x2 - y2))/2
if y2 > x2:
thetai += pi/2
m1 = (x2 + y2)/2
m2 = sqrt(max((x2 - y2)**2/4 + xy**2, 0))
ai = max(1/12, sqrt(max(m1 + m2, 0)))
bi = max(1/12, sqrt(max(m1 - m2, 0)))
if ai/bi > 2:
# Prevent too elongated apertures usually occurring for
# faint objects
bi = ai
else:
# Cannot obtain a,b,theta from isophotal analysis, assume
# circular aperture
ai, bi, thetai, f = radius, radius, 0, 0
a[i] = sources[i]['a'] = ai
b[i] = sources[i]['b'] = bi
theta[i] = sources[i]['theta'] = thetai
flux[i] = sources[i]['flux'] = f
bad = (a < b).nonzero()
a[bad], b[bad] = b[bad], a[bad]
theta[bad] += pi/2
theta %= pi
theta[theta > pi/2] -= pi
elongation = a/b
# Obtain the optimal aperture radius from the brightest non-saturated
# source
if not k:
for i in argsort(flux)[::-1]:
if sep.sum_ellipse(
img >= sat_level, [x[i]], [y[i]], a[i], b[i], theta[i],
1, subpix=0)[0][0]:
# Saturated source
continue
try:
# noinspection PyTypeChecker
res = minimize(
calc_flux_err, [a[i]*1.6],
(img_back, x[i], y[i], elongation[i], theta[i], tmp_rms,
mask, gain), bounds=[(1, None)], tol=1e-5)
except ValueError:
continue
if not res.success:
continue
k = res.x[0]/a[i]
break
if not k:
raise ValueError(
'Not enough data for automatic aperture factor; use '
'explicit aperture factor')
# Calculate weighted median of aperture sizes, elongations, and/or
# orientations if requested
r = sqrt(a*b)*k
if r.size > 1 and any([fix_aper, fix_ell, fix_rot]):
flux[flux < 0] = 0
if not flux.any():
raise ValueError(
'Not enough data for weighted median in fixed-aperture '
'automatic photometry; use static fixed-aperture or fully '
'adaptive automatic photometry instead')
if fix_aper:
r = weighted_median(r, flux)
if fix_ell:
elongation = weighted_median(elongation, flux)
if fix_rot:
theta = weighted_median(theta, flux, period=pi)
if theta > pi/2:
theta -= pi
# Calculate the final aperture and annulus sizes
sqrt_el = sqrt(elongation)
a, b = r*sqrt_el, r/sqrt_el
if not have_background:
if not k_in:
k_in = 1.5*k
if not k_out:
k_out = 2*k
a_in = a*(k_in/k)
a_out, b_out = a*(k_out/k), b*(k_out/k)
theta_out = theta
# Calculate mean and RMS of background; to get the pure sigma, set error
# to 1 and don't pass the gain
if have_background:
if fixed_aper and a == b:
bk_area = sep.sum_circle(area_img, x, y, a, mask=mask, subpix=0)[0]
bk_mean, bk_sigma = sep.sum_circle(
background, x, y, a, err=1, mask=mask, subpix=0)[:2]
else:
bk_area = sep.sum_ellipse(
area_img, x, y, a, b, theta, 1, mask=mask, subpix=0)[0]
bk_mean, bk_sigma = sep.sum_ellipse(
background, x, y, a, b, theta, 1, err=1, mask=mask,
subpix=0)[:2]
error = background_rms
elif fixed_aper and a_out == b_out:
bk_area = sep.sum_circann(
area_img, x, y, a_in, a_out, mask=mask, subpix=0)[0]
bk_mean, bk_sigma = sep.sum_circann(
img, x, y, a_in, a_out, err=1, mask=mask, subpix=0)[:2]
error = bk_sigma
else:
bk_area = sep.sum_ellipann(
area_img, x, y, a_out, b_out, theta_out, a_in/a_out, 1, mask=mask,
subpix=0)[0]
bk_mean, bk_sigma = sep.sum_ellipann(
img, x, y, a_out, b_out, theta_out, a_in/a_out, 1, err=1, mask=mask,
subpix=0)[:2]
error = bk_sigma
if have_background:
area = bk_area
elif fixed_aper and a == b:
area = sep.sum_circle(area_img, x, y, a, mask=mask, subpix=0)[0]
else:
area = sep.sum_ellipse(
area_img, x, y, a, b, theta, 1, mask=mask, subpix=0)[0]
if fixed_aper and a == b:
# Fixed circular aperture
if ndim(error) == 1:
# Separate scalar error for each source
flux, flux_err = empty([2, len(sources)], dtype=float)
flags = empty(len(sources), dtype=int)
for i, (_x, _y, _err) in enumerate(zip(x, y, error)):
flux[i], flux_err[i], flags[i] = sep.sum_circle(
img, [_x], [_y], a, err=_err, mask=mask, gain=gain,
subpix=0)
else:
flux, flux_err, flags = sep.sum_circle(
img, x, y, a, err=error, mask=mask, gain=gain, subpix=0)
else:
# Variable or elliptic aperture
if ndim(error) == 1:
# Separate scalar error for each source
flux, flux_err = empty([2, len(sources)], dtype=float)
flags = empty(len(sources), dtype=int)
if isscalar(a):
a = full_like(x, a)
if isscalar(b):
b = full_like(x, b)
if isscalar(theta):
theta = full_like(x, theta)
for i, (_x, _y, _err, _a, _b, _theta) in enumerate(zip(
x, y, error, a, b, theta)):
flux[i], flux_err[i], flags[i] = sep.sum_ellipse(
img, [_x], [_y], _a, _b, _theta, 1, err=_err, mask=mask,
gain=gain, subpix=0)
else:
flux, flux_err, flags = sep.sum_ellipse(
img, x, y, a, b, theta, 1, err=error, mask=mask, gain=gain,
subpix=0)
# Convert background sum to mean and subtract background from fluxes
if have_background:
# Background area equals aperture area
flux -= bk_mean
bk_mean = bk_mean/area
else:
# Background area equals annulus area
bk_mean = bk_mean/bk_area
flux -= bk_mean*area
# Convert ADUs to electrons
flux *= gain
flux_err *= gain
bk_mean *= gain
bk_sigma *= gain
# Calculate aperture correction for all aperture sizes from the brightest
# source
aper_corr = {}
if apcorr_tol > 0:
for i in argsort(flux)[::-1]:
xi, yi = x[i], y[i]
if isscalar(a):
ai = a
else:
ai = a[i]
if isscalar(b):
bi = b
else:
bi = b[i]
if isscalar(theta):
thetai = theta
else:
thetai = theta[i]
if ndim(error) == 1:
err = error[i]
else:
err = error
if ai == bi:
nsat = sep.sum_circle(
img >= sat_level, [xi], [yi], ai, subpix=0)[0][0]
else:
nsat = sep.sum_ellipse(
img >= sat_level, [xi], [yi], ai, bi, thetai, 1,
subpix=0)[0][0]
if nsat:
# Saturated source
continue
# Obtain total flux by increasing aperture size until it grows
# either more than before (i.e. a nearby source in the aperture) or
# less than the threshold (i.e. the growth curve reached saturation)
f0 = f_prev = flux[i]
dap = 0
f_tot = df_prev = None
while True:
dap += 0.1
if ai == bi:
f, f_err, fl = sep.sum_circle(
img, [xi], [yi], ai + dap, err=err, mask=mask,
gain=gain, subpix=0)
area_i = sep.sum_circle(
area_img, [xi], [yi], ai + dap, mask=mask,
subpix=0)[0][0]
else:
f, f_err, fl = sep.sum_ellipse(
img, [xi], [yi], ai + dap, bi*(1 + dap/ai), thetai, 1,
err=err, mask=mask, gain=gain, subpix=0)
area_i = sep.sum_ellipse(
area_img, [xi], [yi], ai + dap, bi + dap, thetai, 1,
mask=mask, subpix=0)[0][0]
f, fl = f[0], fl[0]
if fl:
break
f = (f - bk_mean[i]*area_i)*gain
if f <= 0:
break
df = f/f_prev
if df_prev is not None and df > df_prev:
# Increasing growth, nearby source hit
f_tot = f_prev
break
if df < 1 + apcorr_tol:
# Growth stopped to within the tolerance
f_tot = f
break
f_prev, df_prev = f, df
if f_tot is None:
continue
# Calculate fluxes for the chosen source for all unique aperture
# sizes used for other sources
fluxes_for_ap = {ai: f0}
if not isscalar(a):
for aj in set(a) - {ai}:
bj = aj*bi/ai
if aj == bj:
f, fl = sep.sum_circle(
img, [xi], [yi], aj, err=err, mask=mask, gain=gain,
subpix=0)[::2]
area_j = sep.sum_circle(
area_img, [xi], [yi], aj, mask=mask, subpix=0)[0][0]
else:
f, fl = sep.sum_ellipse(
img, [xi], [yi], aj, bj, thetai, 1, err=err,
mask=mask, gain=gain, subpix=0)[::2]
area_j = sep.sum_ellipse(
area_img, [xi], [yi], aj, bj, thetai, 1,
mask=mask, subpix=0)[0][0]
f, fl = f[0], fl[0]
f = (f - bk_mean[i]*area_j)*gain
if fl or f <= 0:
continue
fluxes_for_ap[aj] = f
# Calculate aperture corrections
for aj, f in fluxes_for_ap.items():
if f < f_tot:
aper_corr[aj] = -2.5*log10(f_tot/f)
break
if 'flux' in sources.dtype.names:
sources['flux'] = flux
else:
sources = append_fields(sources, 'flux', flux, usemask=False)
if 'flux_err' in sources.dtype.names:
sources['flux_err'] = flux_err
else:
sources = append_fields(sources, 'flux_err', flux_err, usemask=False)
if 'flag' in sources.dtype.names:
sources['flag'] |= flags
else:
sources = append_fields(sources, 'flag', flags, usemask=False)
for name in ['mag', 'mag_err', 'aper_a', 'aper_b', 'aper_theta',
'aper_a_in', 'aper_a_out', 'aper_b_out', 'aper_theta_out',
'aper_area', 'background_area', 'background',
'background_rms']:
if name not in sources.dtype.names:
sources = append_fields(sources, name, z, usemask=False)
good = (flux > 0).nonzero()
if len(good[0]):
sources['mag'][good] = -2.5*log10(flux[good]/texp)
sources['mag_err'][good] = 2.5*log10(1 + flux_err[good]/flux[good])
sources['aper_a'] = a
sources['aper_b'] = b
sources['aper_theta'] = theta
if not have_background:
sources['aper_a_in'] = a_in
sources['aper_a_out'] = a_out
sources['aper_b_out'] = b_out
sources['aper_theta_out'] = theta_out
sources['aper_area'] = area
sources['background_area'] = bk_area
sources['background'] = bk_mean
sources['background_rms'] = bk_sigma
# Apply aperture correction
for i in good[0]:
sources['mag'][i] += aper_corr.get(sources['aper_a'][i], 0)
return sources
def aperture_masses(info,
mass_map,
detect=None,
rad=None,
n_rad=15,
linear=False,
r_min=0.1,
r_max=None,
subpix=5,
**detect_kwargs):
"""Estimate stellar mass profiles based on aperture statistics.
Parameters
----------
info : dict
Basic information of the galaxy.
maps : dict
All the stellar mass maps.
detect : dict
A dictionary that contains the average shape of the galaxy. Default: None.
rad : ndarray, optional
Array of boundaries for radius bins in unit of kpc. Default: None.
n_rad : int, optional
Number of radial bins. Default: 15.
linear : bool, optional
If True, radial bins will be uniformly spaced in linear space.
If False, radial bins will be uniformly spaced in log10 space.
Default: False
r_min : float, optional
Minimum radius of the radial bins. Default: 0.1
r_max : float, optional
Maximum radius of the radial bins. Default: None.
subpix : int, optional
Subpixel sampling factor. Default is 5.
Returns
-------
"""
# If basic information is not available, detect the galaxy here.
if detect is None:
detect = detect_galaxy(info, mass_map, **detect_kwargs)
# Get the radial bins in unit of kpc
if rad is None:
if r_max is None:
r_max = info['img_w'] / 2.0
if linear:
rad = np.linspace(r_min, r_max * info['pix'], (n_rad + 1))
else:
rad = np.logspace(np.log10(r_min), np.log10(r_max * info['pix']),
(n_rad + 1))
# Mass within different apertures
maper = sep.sum_ellipse(mass_map,
detect['x'],
detect['y'],
rad / info['pix'],
rad / info['pix'] * detect['ba'],
detect['theta'],
1.0,
bkgann=None,
subpix=subpix)[0]
return rad, maper
def do_stage(self, images):
for i, image in enumerate(images):
try:
# Set the number of source pixels to be 5% of the total. This keeps us safe from
# satellites and airplanes.
sep.set_extract_pixstack(int(image.nx * image.ny * 0.05))
data = image.data.copy()
error = (np.abs(data) + image.readnoise**2.0)**0.5
mask = image.bpm > 0
# Fits can be backwards byte order, so fix that if need be and subtract
# the background
try:
bkg = sep.Background(data,
mask=mask,
bw=32,
bh=32,
fw=3,
fh=3)
except ValueError:
data = data.byteswap(True).newbyteorder()
bkg = sep.Background(data,
mask=mask,
bw=32,
bh=32,
fw=3,
fh=3)
bkg.subfrom(data)
# Do an initial source detection
# TODO: Add back in masking after we are sure SEP works
sources = sep.extract(data,
self.threshold,
minarea=self.min_area,
err=error,
deblend_cont=0.005)
# Convert the detections into a table
sources = Table(sources)
# Calculate the ellipticity
sources['ellipticity'] = 1.0 - (sources['b'] / sources['a'])
# Fix any value of theta that are invalid due to floating point rounding
# -pi / 2 < theta < pi / 2
sources['theta'][sources['theta'] > (np.pi / 2.0)] -= np.pi
sources['theta'][sources['theta'] < (-np.pi / 2.0)] += np.pi
# Calculate the kron radius
kronrad, krflag = sep.kron_radius(data, sources['x'],
sources['y'], sources['a'],
sources['b'],
sources['theta'], 6.0)
sources['flag'] |= krflag
sources['kronrad'] = kronrad
# Calcuate the equivilent of flux_auto
flux, fluxerr, flag = sep.sum_ellipse(data,
sources['x'],
sources['y'],
sources['a'],
sources['b'],
np.pi / 2.0,
2.5 * kronrad,
subpix=1,
err=error)
sources['flux'] = flux
sources['fluxerr'] = fluxerr
sources['flag'] |= flag
# Calculate the FWHMs of the stars:
fwhm = 2.0 * (np.log(2) *
(sources['a']**2.0 + sources['b']**2.0))**0.5
sources['fwhm'] = fwhm
# Cut individual bright pixels. Often cosmic rays
sources = sources[fwhm > 1.0]
# Measure the flux profile
flux_radii, flag = sep.flux_radius(data,
sources['x'],
sources['y'],
6.0 * sources['a'],
[0.25, 0.5, 0.75],
normflux=sources['flux'],
subpix=5)
sources['flag'] |= flag
sources['fluxrad25'] = flux_radii[:, 0]
sources['fluxrad50'] = flux_radii[:, 1]
sources['fluxrad75'] = flux_radii[:, 2]
# Calculate the windowed positions
sig = 2.0 / 2.35 * sources['fluxrad50']
xwin, ywin, flag = sep.winpos(data, sources['x'], sources['y'],
sig)
sources['flag'] |= flag
sources['xwin'] = xwin
sources['ywin'] = ywin
# Calculate the average background at each source
bkgflux, fluxerr, flag = sep.sum_ellipse(bkg.back(),
sources['x'],
sources['y'],
sources['a'],
sources['b'],
np.pi / 2.0,
2.5 *
sources['kronrad'],
subpix=1)
#masksum, fluxerr, flag = sep.sum_ellipse(mask, sources['x'], sources['y'],
# sources['a'], sources['b'], np.pi / 2.0,
# 2.5 * kronrad, subpix=1)
background_area = (
2.5 * sources['kronrad']
)**2.0 * sources['a'] * sources['b'] * np.pi # - masksum
sources['background'] = bkgflux
sources['background'][background_area > 0] /= background_area[
background_area > 0]
# Update the catalog to match fits convention instead of python array convention
sources['x'] += 1.0
sources['y'] += 1.0
sources['xpeak'] += 1
sources['ypeak'] += 1
sources['xwin'] += 1.0
sources['ywin'] += 1.0
sources['theta'] = np.degrees(sources['theta'])
image.catalog = sources['x', 'y', 'xwin', 'ywin', 'xpeak',
'ypeak', 'flux', 'fluxerr',
'background', 'fwhm', 'a', 'b',
'theta', 'kronrad', 'ellipticity',
'fluxrad25', 'fluxrad50', 'fluxrad75',
'x2', 'y2', 'xy', 'flag']
# Add the units and description to the catalogs
image.catalog['x'].unit = 'pixel'
image.catalog['x'].description = 'X coordinate of the object'
image.catalog['y'].unit = 'pixel'
image.catalog['y'].description = 'Y coordinate of the object'
image.catalog['xwin'].unit = 'pixel'
image.catalog[
'xwin'].description = 'Windowed X coordinate of the object'
image.catalog['ywin'].unit = 'pixel'
image.catalog[
'ywin'].description = 'Windowed Y coordinate of the object'
image.catalog['xpeak'].unit = 'pixel'
image.catalog['xpeak'].description = 'X coordinate of the peak'
image.catalog['ypeak'].unit = 'pixel'
image.catalog[
'ypeak'].description = 'Windowed Y coordinate of the peak'
image.catalog['flux'].unit = 'counts'
image.catalog[
'flux'].description = 'Flux within a Kron-like elliptical aperture'
image.catalog['fluxerr'].unit = 'counts'
image.catalog[
'fluxerr'].description = 'Erronr on the flux within a Kron-like elliptical aperture'
image.catalog['background'].unit = 'counts'
image.catalog[
'background'].description = 'Average background value in the aperture'
image.catalog['fwhm'].unit = 'pixel'
image.catalog['fwhm'].description = 'FWHM of the object'
image.catalog['a'].unit = 'pixel'
image.catalog[
'a'].description = 'Semi-major axis of the object'
image.catalog['b'].unit = 'pixel'
image.catalog[
'b'].description = 'Semi-minor axis of the object'
image.catalog['theta'].unit = 'degrees'
image.catalog[
'theta'].description = 'Position angle of the object'
image.catalog['kronrad'].unit = 'pixel'
image.catalog[
'kronrad'].description = 'Kron radius used for extraction'
image.catalog['ellipticity'].description = 'Ellipticity'
image.catalog['fluxrad25'].unit = 'pixel'
image.catalog[
'fluxrad25'].description = 'Radius containing 25% of the flux'
image.catalog['fluxrad50'].unit = 'pixel'
image.catalog[
'fluxrad50'].description = 'Radius containing 50% of the flux'
image.catalog['fluxrad75'].unit = 'pixel'
image.catalog[
'fluxrad75'].description = 'Radius containing 75% of the flux'
image.catalog['x2'].unit = 'pixel^2'
image.catalog[
'x2'].description = 'Variance on X coordinate of the object'
image.catalog['y2'].unit = 'pixel^2'
image.catalog[
'y2'].description = 'Variance on Y coordinate of the object'
image.catalog['xy'].unit = 'pixel^2'
image.catalog['xy'].description = 'XY covariance of the object'
image.catalog[
'flag'].description = 'Bit mask combination of extraction and photometry flags'
image.catalog.sort('flux')
image.catalog.reverse()
logging_tags = logs.image_config_to_tags(
image, self.group_by_keywords)
logs.add_tag(logging_tags, 'filename',
os.path.basename(image.filename))
# Save some background statistics in the header
mean_background = stats.sigma_clipped_mean(bkg.back(), 5.0)
image.header['L1MEAN'] = (
mean_background,
'[counts] Sigma clipped mean of frame background')
logs.add_tag(logging_tags, 'L1MEAN', float(mean_background))
median_background = np.median(bkg.back())
image.header['L1MEDIAN'] = (
median_background, '[counts] Median of frame background')
logs.add_tag(logging_tags, 'L1MEDIAN',
float(median_background))
std_background = stats.robust_standard_deviation(bkg.back())
image.header['L1SIGMA'] = (
std_background,
'[counts] Robust std dev of frame background')
logs.add_tag(logging_tags, 'L1SIGMA', float(std_background))
# Save some image statistics to the header
good_objects = image.catalog['flag'] == 0
seeing = np.median(
image.catalog['fwhm'][good_objects]) * image.pixel_scale
image.header['L1FWHM'] = (seeing,
'[arcsec] Frame FWHM in arcsec')
logs.add_tag(logging_tags, 'L1FWHM', float(seeing))
mean_ellipticity = stats.sigma_clipped_mean(
sources['ellipticity'][good_objects], 3.0)
image.header['L1ELLIP'] = (mean_ellipticity,
'Mean image ellipticity (1-B/A)')
logs.add_tag(logging_tags, 'L1ELLIP', float(mean_ellipticity))
mean_position_angle = stats.sigma_clipped_mean(
sources['theta'][good_objects], 3.0)
image.header['L1ELLIPA'] = (
mean_position_angle, '[deg] PA of mean image ellipticity')
logs.add_tag(logging_tags, 'L1ELLIPA',
float(mean_position_angle))
self.logger.info('Extracted sources', extra=logging_tags)
except Exception as e:
logging_tags = logs.image_config_to_tags(
image, self.group_by_keywords)
logs.add_tag(logging_tags, 'filename',
os.path.basename(image.filename))
self.logger.error(e, extra=logging_tags)
return images
def _run_sep(self):
import sep
# THRESH=1.2 # in sky sigma
# DETECT_THRESH=1.6 # in sky sigma
# DEBLEND_MINCONT=0.005
# DETECT_MINAREA = 6 # minimum number of pixels above threshold
objs, seg = sep.extract(
self.detim,
self.detect_thresh,
err=self.detnoise,
segmentation_map=True,
**self.sx_config
)
logger.debug('found %d objects' % objs.size)
if objs.size == 0:
self.cat = objs
return None
flux_auto = np.zeros(objs.size)-9999.0
fluxerr_auto = np.zeros(objs.size)-9999.0
flux_radius = np.zeros(objs.size)-9999.0
kron_radius = np.zeros(objs.size)-9999.0
w, = np.where(
(objs['a'] >= 0.0) &
(objs['b'] >= 0.0) &
between(objs['theta'], -pi/2., pi/2., type='[]')
)
if w.size > 0:
kron_radius[w], krflag = sep.kron_radius(
self.detim,
objs['x'][w],
objs['y'][w],
objs['a'][w],
objs['b'][w],
objs['theta'][w],
6.0,
)
objs['flag'][w] |= krflag
aper_rad = 2.5*kron_radius
flux_auto[w], fluxerr_auto[w], flag_auto = \
sep.sum_ellipse(
self.detim,
objs['x'][w],
objs['y'][w],
objs['a'][w],
objs['b'][w],
objs['theta'][w],
aper_rad[w],
subpix=1,
)
objs['flag'][w] |= flag_auto
# what we did in DES, but note threshold above
# is 1 as opposed to wide survey. deep survey
# was even lower, 0.8?
# used half light radius
PHOT_FLUXFRAC = 0.5
flux_radius[w], frflag = sep.flux_radius(
self.detim,
objs['x'][w],
objs['y'][w],
6.*objs['a'][w],
PHOT_FLUXFRAC,
normflux=flux_auto[w],
subpix=5,
)
objs['flag'][w] |= frflag # combine flags into 'flag'
ncut = 2 # need this to make sure array
new_dt = [
('id', 'i8'),
('number', 'i4'),
('ncutout', 'i4'),
('kron_radius', 'f4'),
('flux_auto', 'f4'),
('fluxerr_auto', 'f4'),
('flux_radius', 'f4'),
('isoarea_image', 'f4'),
('iso_radius', 'f4'),
('box_size', 'i4'),
('file_id', 'i8', ncut),
('orig_row', 'f4', ncut),
('orig_col', 'f4', ncut),
('orig_start_row', 'i8', ncut),
('orig_start_col', 'i8', ncut),
('orig_end_row', 'i8', ncut),
('orig_end_col', 'i8', ncut),
('cutout_row', 'f4', ncut),
('cutout_col', 'f4', ncut),
('dudrow', 'f8', ncut),
('dudcol', 'f8', ncut),
('dvdrow', 'f8', ncut),
('dvdcol', 'f8', ncut),
]
cat = eu.numpy_util.add_fields(objs, new_dt)
cat['id'] = np.arange(cat.size)
cat['number'] = np.arange(1, cat.size+1)
cat['ncutout'] = 1
cat['flux_auto'] = flux_auto
cat['fluxerr_auto'] = fluxerr_auto
cat['flux_radius'] = flux_radius
wcs = self.datalist[0]['wcs']
cat['dudrow'][:, 0] = wcs.dudy
cat['dudcol'][:, 0] = wcs.dudx
cat['dvdrow'][:, 0] = wcs.dvdy
cat['dvdcol'][:, 0] = wcs.dvdx
# use the number of pixels in the seg map as the iso area
for i in range(objs.size):
w = np.where(seg == (i+1))
cat['isoarea_image'][i] = w[0].size
cat['iso_radius'] = np.sqrt(cat['isoarea_image'].clip(min=1)/np.pi)
box_size = self._get_box_sizes(cat)
half_box_size = box_size//2
maxrow, maxcol = self.detim.shape
cat['box_size'] = box_size
cat['orig_row'][:, 0] = cat['y']
cat['orig_col'][:, 0] = cat['x']
orow = cat['orig_row'][:, 0].astype('i4')
ocol = cat['orig_col'][:, 0].astype('i4')
ostart_row = orow - half_box_size + 1
ostart_col = ocol - half_box_size + 1
oend_row = orow + half_box_size + 1 # plus one for slices
oend_col = ocol + half_box_size + 1
ostart_row.clip(min=0, out=ostart_row)
ostart_col.clip(min=0, out=ostart_col)
oend_row.clip(max=maxrow, out=oend_row)
oend_col.clip(max=maxcol, out=oend_col)
# could result in smaller than box_size above
cat['orig_start_row'][:, 0] = ostart_row
cat['orig_start_col'][:, 0] = ostart_col
cat['orig_end_row'][:, 0] = oend_row
cat['orig_end_col'][:, 0] = oend_col
cat['cutout_row'][:, 0] = \
cat['orig_row'][:, 0] - cat['orig_start_row'][:, 0]
cat['cutout_col'][:, 0] = \
cat['orig_col'][:, 0] - cat['orig_start_col'][:, 0]
self.seg = seg
self.bmask = np.zeros(seg.shape, dtype='i4')
self.cat = cat
def test_vs_sextractor():
data = np.copy(image_data) # make an explicit copy so we can 'subfrom'
bkg = sep.Background(data, bw=64, bh=64, fw=3, fh=3)
# Test that SExtractor background is same as SEP:
bkgarr = bkg.back(dtype=np.float32)
assert_allclose(bkgarr, image_refback, rtol=1.e-5)
# Extract objects
bkg.subfrom(data)
objs = sep.extract(data, 1.5*bkg.globalrms)
objs = np.sort(objs, order=['y'])
# Read SExtractor result
refobjs = np.loadtxt(IMAGECAT_FNAME, dtype=IMAGECAT_DTYPE)
refobjs = np.sort(refobjs, order=['y'])
# Found correct number of sources at the right locations?
assert_allclose(objs['x'], refobjs['x'] - 1., atol=1.e-3)
assert_allclose(objs['y'], refobjs['y'] - 1., atol=1.e-3)
# Test aperture flux
flux, fluxerr, flag = sep.sum_circle(data, objs['x'], objs['y'], 5.,
err=bkg.globalrms)
assert_allclose(flux, refobjs['flux_aper'], rtol=2.e-4)
assert_allclose(fluxerr, refobjs['fluxerr_aper'], rtol=1.0e-5)
# check if the flags work at all (comparison values
assert ((flag & sep.APER_TRUNC) != 0).sum() == 4
assert ((flag & sep.APER_HASMASKED) != 0).sum() == 0
# Test "flux_auto"
kr, flag = sep.kron_radius(data, objs['x'], objs['y'], objs['a'],
objs['b'], objs['theta'], 6.0)
flux, fluxerr, flag = sep.sum_ellipse(data, objs['x'], objs['y'],
objs['a'], objs['b'],
objs['theta'], r=2.5 * kr,
err=bkg.globalrms, subpix=1)
# For some reason, object at index 59 doesn't match. It's very small
# and kron_radius is set to 0.0 in SExtractor, but 0.08 in sep.
# Most of the other values are within 1e-4 except one which is only
# within 0.01. This might be due to a change in SExtractor between
# v2.8.6 (used to generate "truth" catalog) and v2.18.11.
kr[59] = 0.0
flux[59] = 0.0
fluxerr[59] = 0.0
assert_allclose(2.5*kr, refobjs['kron_radius'], rtol=0.01)
assert_allclose(flux, refobjs['flux_auto'], rtol=0.01)
assert_allclose(fluxerr, refobjs['fluxerr_auto'], rtol=0.01)
# Test ellipse representation conversion
cxx, cyy, cxy = sep.ellipse_coeffs(objs['a'], objs['b'], objs['theta'])
assert_allclose(cxx, objs['cxx'], rtol=1.e-4)
assert_allclose(cyy, objs['cyy'], rtol=1.e-4)
assert_allclose(cxy, objs['cxy'], rtol=1.e-4)
a, b, theta = sep.ellipse_axes(objs['cxx'], objs['cyy'], objs['cxy'])
assert_allclose(a, objs['a'], rtol=1.e-4)
assert_allclose(b, objs['b'], rtol=1.e-4)
assert_allclose(theta, objs['theta'], rtol=1.e-4)
#test round trip
cxx, cyy, cxy = sep.ellipse_coeffs(a, b, theta)
assert_allclose(cxx, objs['cxx'], rtol=1.e-4)
assert_allclose(cyy, objs['cyy'], rtol=1.e-4)
assert_allclose(cxy, objs['cxy'], rtol=1.e-4)
# test flux_radius
fr, flags = sep.flux_radius(data, objs['x'], objs['y'], 6.*refobjs['a'],
[0.1, 0.5, 0.6], normflux=refobjs['flux_auto'],
subpix=5)
assert_allclose(fr, refobjs["flux_radius"], rtol=0.04, atol=0.01)
# test winpos
sig = 2. / 2.35 * fr[:, 1] # flux_radius = 0.5
xwin, ywin, flag = sep.winpos(data, objs['x'], objs['y'], sig)
assert_allclose(xwin, refobjs["xwin"] - 1., rtol=0., atol=0.0025)
assert_allclose(ywin, refobjs["ywin"] - 1., rtol=0., atol=0.0025)
naper = 1000
nloop = 1
a = 1.
b = 1.
theta = np.pi / 4.
for r in r_list:
for subpix, method, label in subpix_list:
line = "| ellipses r={0:2d} {1:8s} |".format(int(r), label)
t0 = time.time()
flux, fluxerr, flag = sep.sum_ellipse(data,
x,
y,
a,
b,
theta,
r,
subpix=subpix)
t1 = time.time()
t_sep = (t1 - t0) * 1.e6 / naper / nloop
line += " {0:7.2f} us/aper |".format(t_sep)
if HAVE_PHOTUTILS:
apertures = photutils.EllipticalAperture((x, y), a * r, b * r,
theta)
t0 = time.time()
res = photutils.aperture_photometry(data,
apertures,
method=method,
subpixels=subpix)
def flux_radius(components, observation=None, frac=0.5, weight_order=0):
"""
Determine the radius R (in pixels, along semi-major axis),
the flux within R has a fraction of `frac` over the total flux.
Parameters
----------
components: a list of `scarlet.Component` or `scarlet.ComponentTree`
Component to analyze
observation:
frac: float
fraction of lights within this R.
"""
from scipy.interpolate import interp1d, UnivariateSpline
if not isinstance(components, list):
components = [components]
# Determine the centroid, averaged through channels
_, y_cen, x_cen = centroid(components, observation=observation)
s = shape(components,
observation,
show_fig=False,
weight_order=weight_order)
q = s['q']
theta = np.deg2rad(s['pa'])
blend = scarlet.Blend(components, observation)
model = blend.get_model()
mask = (observation.weights == 0)
model = model * ~mask
total_flux = model.sum(axis=(1, 2))
depth = model.shape[0]
r_frac = []
## sep.sum_ellipse is very slow! Try to improve!
if depth > 1:
for i in range(depth):
r_max = max(model.shape)
r_ = np.linspace(0, r_max, 500)
flux_ = sep.sum_ellipse(model[i],
x_cen,
y_cen,
1,
1 * q[i],
theta[i],
r=r_)[0]
flux_ /= total_flux[i]
func = UnivariateSpline(r_, flux_ - frac, s=0)
r_frac.append(func.roots()[0])
else: # might be buggy
r_max = max(model.shape)
r_ = np.linspace(0, r_max, 500)
flux_ = sep.sum_ellipse(model[0],
x_cen,
y_cen,
1,
1 * q[0],
theta[0],
r=r_)[0]
flux_ /= total_flux[0]
func = UnivariateSpline(r_, flux_ - frac, s=0)
r_frac.append(func.roots()[0])
return np.array(r_frac)
def detect_with_sep(event,
detect_thresh=2.,
npixels=8,
grow_seg=5,
gauss_fwhm=2.,
gsize=3,
im_wcs=None,
root='mycat'):
drz_file = event['fits_s3_key']
drz_file_bucket = event['fits_s3_bucket']
root = drz_file.split('/')[-1].split('_')[0]
s3 = boto3.resource('s3')
s3_client = boto3.client('s3')
bkt = s3.Bucket(drz_file_bucket)
bkt.download_file(drz_file,
'/tmp/{0}'.format(root),
ExtraArgs={"RequestPayer": "requester"})
im = fits.open('/tmp/{0}'.format(root))
im_wcs = wcs.WCS(im[1].header, relax=True)
data = im[1].data.byteswap().newbyteorder()
wht_data = im[2].data.byteswap().newbyteorder()
data_mask = np.cast[data.dtype](data == 0)
## Get AB zeropoint
if 'PHOTFNU' in im[0].header:
ZP = -2.5 * np.log10(im[0].header['PHOTFNU']) + 8.90
elif 'PHOTFLAM' in im[0].header:
ZP = (-2.5 * np.log10(im[0].header['PHOTFLAM']) - 21.10 -
5 * np.log10(im[0].header['PHOTPLAM']) + 18.6921)
else:
print(
'Couldn\'t find PHOTFNU or PHOTPLAM/PHOTFLAM keywords, use ZP=25')
return None
# Scale fluxes to mico-Jy
uJy_to_dn = 1 / (3631 * 1e6 * 10**(-0.4 * ZP))
err = 1 / np.sqrt(wht_data)
# set up the error array
err = 1 / np.sqrt(wht_data)
err[~np.isfinite(err)] = 0
mask = (err == 0)
# get the background
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
bkg_data = bkg.back()
ratio = bkg.rms() / err
err_scale = np.median(ratio[(~mask) & np.isfinite(ratio)])
err *= err_scale
objects = sep.extract(data - bkg_data,
detect_thresh,
err=err,
mask=mask,
minarea=14,
filter_kernel=GAUSS_3_7x7,
filter_type='conv',
deblend_nthresh=32,
deblend_cont=0.005,
clean=True,
clean_param=1.,
segmentation_map=False)
catalog = Table(objects)
# add things to catalog
autoparams = [2.5, 3.5]
catalog['number'] = np.arange(len(catalog), dtype=np.int32) + 1
catalog['theta'] = np.clip(catalog['theta'], -np.pi / 2, np.pi / 2)
for c in ['a', 'b', 'x', 'y', 'theta']:
catalog = catalog[np.isfinite(catalog[c])]
catalog['ra'], catalog['dec'] = im_wcs.all_pix2world(
catalog['x'], catalog['y'], 1)
catalog['ra'].unit = u.deg
catalog['dec'].unit = u.deg
catalog['x_world'], catalog['y_world'] = catalog['ra'], catalog['dec']
kronrad, krflag = sep.kron_radius(data - bkg_data, catalog['x'],
catalog['y'], catalog['a'], catalog['b'],
catalog['theta'], 6.0)
kronrad *= autoparams[0]
kronrad[~np.isfinite(kronrad)] = autoparams[1]
kronrad = np.maximum(kronrad, autoparams[1])
kron_out = sep.sum_ellipse(data - bkg_data,
catalog['x'],
catalog['y'],
catalog['a'],
catalog['b'],
catalog['theta'],
kronrad,
subpix=5,
err=err)
kron_flux, kron_fluxerr, kron_flag = kron_out
kron_flux_flag = kron_flag
catalog['mag_auto_raw'] = ZP - 2.5 * np.log10(kron_flux)
catalog['magerr_auto_raw'] = 2.5 / np.log(10) * kron_fluxerr / kron_flux
catalog['mag_auto'] = catalog['mag_auto_raw'] * 1.
catalog['magerr_auto'] = catalog['magerr_auto_raw'] * 1.
catalog['kron_radius'] = kronrad * u.pixel
catalog['kron_flag'] = krflag
catalog['kron_flux_flag'] = kron_flux_flag
# Make a plot
im_data = im[1].data
im_shape = im_data.shape
im_data[np.isnan(im_data)] = 0.0
# Trim the top and bottom 1 percent of pixel values
top = np.percentile(im_data, 99)
im_data[im_data > top] = top
bottom = np.percentile(im_data, 1)
im_data[im_data < bottom] = bottom
# Scale the data.
im_data = im_data - im_data.min()
im_data = (im_data / im_data.max()) * 255.
im_data = np.uint8(im_data)
f, (ax) = plt.subplots(1, 1, sharex=True)
f.set_figheight(12)
f.set_figwidth(12)
ax.imshow(im_data, cmap="Greys", clim=(0, 255), origin='lower')
ax.plot(catalog['x'],
catalog['y'],
'o',
markeredgewidth=1,
markeredgecolor='red',
markerfacecolor='None')
ax.set_xlim([-0.05 * im_shape[1], 1.05 * im_shape[1]])
ax.set_ylim([-0.05 * im_shape[0], 1.05 * im_shape[0]])
f.savefig('/tmp/{0}.png'.format(root))
# Write the catalog to local disk
catalog.write('/tmp/{0}.catalog.fits'.format(root), format='fits')
# Write out to S3
s3 = boto3.resource('s3')
s3.meta.client.upload_file('/tmp/{0}.catalog.fits'.format(root),
event['s3_output_bucket'],
'{0}/{1}.catalog.fits'.format(root, root))
s3.meta.client.upload_file('/tmp/{0}.png'.format(root),
event['s3_output_bucket'],
'PNG/{0}.png'.format(root))
def find_stars(self, image: Image) -> Table:
"""Find stars in given image and append catalog.
Args:
image: Image to find stars in.
Returns:
Full table with results.
"""
import sep
# get data and make it continuous
data = image.data.copy()
# mask?
mask = image.mask.data if image.mask is not None else None
# estimate background, probably we need to byte swap, and subtract it
try:
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
except ValueError as e:
data = data.byteswap(True).newbyteorder()
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
bkg.subfrom(data)
# extract sources
try:
sources = sep.extract(data, self.threshold, err=bkg.globalrms, minarea=self.minarea,
deblend_nthresh=self.deblend_nthresh, deblend_cont=self.deblend_cont,
clean=self.clean, clean_param=self.clean_param, mask=mask)
except:
log.exception('An error has occured.')
return Table()
# convert to astropy table
sources = Table(sources)
# only keep sources with detection flag < 8
sources = sources[sources['flag'] < 8]
# Calculate the ellipticity
sources['ellipticity'] = 1.0 - (sources['b'] / sources['a'])
# calculate the FWHMs of the stars
fwhm = 2.0 * (np.log(2) * (sources['a'] ** 2.0 + sources['b'] ** 2.0)) ** 0.5
sources['fwhm'] = fwhm
# get gain
gain = image.header['DET-GAIN'] if 'DET-GAIN' in image.header else None
# Kron radius
kronrad, krflag = sep.kron_radius(data, sources['x'], sources['y'], sources['a'], sources['b'],
sources['theta'], 6.0)
sources['flag'] |= krflag
sources['kronrad'] = kronrad
# equivalent of FLUX_AUTO
flux, fluxerr, flag = sep.sum_ellipse(data, sources['x'], sources['y'], sources['a'], sources['b'],
sources['theta'], 2.5 * kronrad, subpix=1, mask=mask,
err=bkg.rms(), gain=gain)
sources['flag'] |= flag
sources['flux'] = flux
sources['fluxerr'] = fluxerr
# radii at 0.25, 0.5, and 0.75 flux
flux_radii, flag = sep.flux_radius(data, sources['x'], sources['y'], 6.0 * sources['a'], [0.25, 0.5, 0.75],
normflux=sources['flux'], subpix=5)
sources['flag'] |= flag
sources['fluxrad25'] = flux_radii[:, 0]
sources['fluxrad50'] = flux_radii[:, 1]
sources['fluxrad75'] = flux_radii[:, 2]
# xwin/ywin
sig = 2. / 2.35 * sources['fluxrad50']
xwin, ywin, flag = sep.winpos(data, sources['x'], sources['y'], sig)
sources['flag'] |= flag
sources['xwin'] = xwin
sources['ywin'] = ywin
# perform aperture photometry for diameters of 1" to 8"
for diameter in [1, 2, 3, 4, 5, 6, 7, 8]:
flux, fluxerr, flag = sep.sum_circle(data, sources['x'], sources['y'],
diameter / 2. / image.pixel_scale,
mask=mask, err=bkg.rms(), gain=gain)
sources['fluxaper{0}'.format(diameter)] = flux
sources['fluxerr{0}'.format(diameter)] = fluxerr
sources['flag'] |= flag
# average background at each source
# since SEP sums up whole pixels, we need to do the same on an image of ones for the background_area
bkgflux, fluxerr, flag = sep.sum_ellipse(bkg.back(), sources['x'], sources['y'],
sources['a'], sources['b'], np.pi / 2.0,
2.5 * sources['kronrad'], subpix=1)
background_area, _, _ = sep.sum_ellipse(np.ones(shape=bkg.back().shape), sources['x'], sources['y'],
sources['a'], sources['b'], np.pi / 2.0,
2.5 * sources['kronrad'], subpix=1)
sources['background'] = bkgflux
sources['background'][background_area > 0] /= background_area[background_area > 0]
# match fits conventions
sources['x'] += 1.0
sources['xpeak'] += 1
sources['xwin'] += 1.0
sources['xmin'] += 1
sources['xmax'] += 1
sources['y'] += 1.0
sources['ypeak'] += 1
sources['ywin'] += 1.0
sources['ymin'] += 1
sources['ymax'] += 1
sources['theta'] = np.degrees(sources['theta'])
# pick columns for catalog
cat = sources['x', 'y', 'xwin', 'ywin', 'xpeak', 'ypeak',
'flux', 'fluxerr', 'peak', 'fluxaper1', 'fluxerr1',
'fluxaper2', 'fluxerr2', 'fluxaper3', 'fluxerr3',
'fluxaper4', 'fluxerr4', 'fluxaper5', 'fluxerr5',
'fluxaper6', 'fluxerr6', 'fluxaper7', 'fluxerr7',
'fluxaper8', 'fluxerr8', 'background', 'fwhm',
'a', 'b', 'theta', 'kronrad', 'ellipticity',
'fluxrad25', 'fluxrad50', 'fluxrad75',
'x2', 'y2', 'xy', 'flag']
# set it
image.catalog = cat
# return full catalog
return sources
def AutoPhot(self, Kron_fact=2.5, min_diameter=3.5, write=True):
kronrad, krflag = sep.kron_radius(self.dat, self.src['x'],
self.src['y'], self.src['a'],
self.src['b'], self.src['theta'], 6.)
kronrad[np.isnan(kronrad) == True] = 0.
flux, fluxerr, flag = sep.sum_ellipse(self.dat,
self.src['x'],
self.src['y'],
self.src['a'],
self.src['b'],
self.src['theta'],
Kron_fact * kronrad,
err=self.skysigma,
gain=self.gain,
subpix=0)
flag |= krflag # Combining flags
r_min = 0.5 * min_diameter
use_circle = kronrad * np.sqrt(self.src['a'] * self.src['b']) < r_min
cflux, cfluxerr, cflag = sep.sum_circle(self.dat,
self.src['x'][use_circle],
self.src['y'][use_circle],
r_min,
err=self.skysigma,
gain=self.gain,
subpix=0)
flux[use_circle] = cflux
fluxerr[use_circle] = cfluxerr
flag[use_circle] = cflag
mag = self.zmag - 2.5 * np.log10(flux)
magerr = (2.5 / np.log(10.0)) * (fluxerr / flux)
r, flag = sep.flux_radius(self.dat,
self.src['x'],
self.src['y'],
6.0 * self.src['a'],
0.5,
normflux=flux,
subpix=5)
ra, dec = self.wcs.all_pix2world(self.src['x'] + 1, self.src['y'] + 1,
1)
df = pd.DataFrame(
data={
'x': self.src['x'],
'y': self.src['y'],
'ra': ra,
'dec': dec,
'a': self.src['a'],
'b': self.src['b'],
'theta': self.src['theta'],
'flux': flux,
'e_flux': fluxerr,
'mag': mag,
'e_mag': magerr,
'kronrad': kronrad,
'flxrad': r,
'flag': flag
})
if write:
df.to_csv(ip.tmp_dir + 'auto_' + self.img.split('.fits')[0] +
'.csv')
f = open(ip.tmp_dir + 'src_' + self.img.split('.fits')[0] + '.reg',
'w')
for i in np.arange(self.nsrc):
f.write('{0:.3f} {1:.3f}\n'.format(self.src['x'][i] + 1,
self.src['y'][i] + 1))
f.close()
return df
def test_masked_segmentation_measurements():
"""Test measurements with segmentation masking"""
NX = 100
data = np.zeros((NX * 2, NX * 2))
yp, xp = np.indices(data.shape)
####
# Make two 2D gaussians that slightly overlap
# width of the 2D objects
gsigma = 10.
# offset between two gaussians in sigmas
off = 4
for xy in [[NX, NX], [NX + off * gsigma, NX + off * gsigma]]:
R = np.sqrt((xp - xy[0])**2 + (yp - xy[1])**2)
g_i = np.exp(-R**2 / 2 / gsigma**2)
data += g_i
# Absolute total
total_exact = g_i.sum()
# Add some noise
rms = 0.02
np.random.seed(1)
data += np.random.normal(size=data.shape) * rms
# Run source detection
objs, segmap = sep.extract(data,
thresh=1.2,
err=rms,
mask=None,
segmentation_map=True)
seg_id = np.arange(1, len(objs) + 1, dtype=np.int32)
# Compute Kron/Auto parameters
x, y, a, b = objs['x'], objs['y'], objs['a'], objs['b']
theta = objs['theta']
kronrad, krflag = sep.kron_radius(data, x, y, a, b, theta, 6.0)
flux_auto, fluxerr, flag = sep.sum_ellipse(data,
x,
y,
a,
b,
theta,
2.5 * kronrad,
segmap=segmap,
seg_id=seg_id,
subpix=1)
# Test total flux
assert_allclose(flux_auto, total_exact, rtol=5.e-2)
# Flux_radius
for flux_fraction in [0.2, 0.5]:
# Exact solution
rhalf_exact = np.sqrt(-np.log(1 - flux_fraction) * gsigma**2 * 2)
# Masked measurement
flux_radius, flag = sep.flux_radius(data,
x,
y,
6. * a,
flux_fraction,
seg_id=seg_id,
segmap=segmap,
normflux=flux_auto,
subpix=5)
# Test flux fraction
assert_allclose(flux_radius, rhalf_exact, rtol=5.e-2)
if False:
print('test_masked_flux_radius')
print(total_exact, flux_auto)
print(rhalf_exact, flux_radius)
def _measure(self, img, sources, mask=None):
logger.info('measuring source parameters')
# HACK: issues with numerical precision
# must have pi/2 <= theta <= npi/2
sources[np.abs(np.abs(sources['theta']) -
np.pi / 2) < 1e-6] = np.pi / 2
for p in ['x', 'y', 'a', 'b', 'theta']:
sources = sources[~np.isnan(sources[p])]
# calculate "AUTO" parameters
kronrad, krflag = sep.kron_radius(img,
sources['x'],
sources['y'],
sources['a'],
sources['b'],
sources['theta'],
6.0,
mask=mask)
flux, fluxerr, flag = sep.sum_ellipse(img,
sources['x'],
sources['y'],
sources['a'],
sources['b'],
sources['theta'],
2.5 * kronrad,
subpix=5,
mask=mask)
flag |= krflag # combine flags into 'flag'
sources = sources[~np.isnan(flux)]
flux = flux[~np.isnan(flux)]
sources = sources[flux > 0]
flux = flux[flux > 0]
mag_auto = self.zpt - 2.5 * np.log10(flux)
r, flag = sep.flux_radius(img,
sources['x'],
sources['y'],
6. * sources['a'],
0.5,
normflux=flux,
subpix=5,
mask=mask)
sources['mag_auto'] = mag_auto
sources['flux_auto'] = flux
sources['flux_radius'] = r * self.pixscale
# approximate fwhm
r_squared = sources['a']**2 + sources['b']**2
sources['fwhm'] = 2 * np.sqrt(np.log(2) * r_squared) * self.pixscale
q = sources['b'] / sources['a']
area = np.pi * q * sources['flux_radius']**2
sources['mu_ave_auto'] = sources['mag_auto'] + 2.5 * np.log10(2 * area)
area_arcsec = np.pi * (self.psf_fwhm / 2)**2 * self.pixscale**2
flux, fluxerr, flag = sep.sum_circle(img,
sources['x'],
sources['y'],
self.psf_fwhm / 2,
subpix=5,
mask=mask)
flux[flux <= 0] = np.nan
mu_0 = self.zpt - 2.5 * np.log10(flux / area_arcsec)
sources['mu_0_aper'] = mu_0
return sources
def sourcephot(catalogue,image,segmap,detection,instrument='MUSE',dxp=0.,dyp=0.,
noise=[False],zpab=False, kn=2.5, circap=1.0):
"""
Get a source catalogue from findsources and a fits image with ZP
and compute magnitudes in that filter
catalogue -> source cat from findsources
image -> fits image with ZP in header
segmap -> fits of segmentation map
detection -> the detection image, used to compute Kron radius
instrument -> if not MUSE, map positions from detection to image
dxp,dyp -> shifts in pixel of image to register MUSE and image astrometry
noise -> if set to a noise model, use equation noise[0]*noise[1]*npix**noise[2]
to compute the error
zpab -> if ZPAB (zeropoint AB) not stored in header, must be supplied
kn -> factor to be used when scaling Kron apertures [sextractor default 2.5]
circap -> radius in arcsec for aperture photmetry to be used when Kron aperture fails
"""
from astropy.io import fits
import numpy as np
import sep
import matplotlib.pyplot as plt
from astropy.table import Table
from astropy import wcs
#grab root name
rname=((image.split('/')[-1]).split('.fits'))[0]
print ('Working on {}'.format(rname))
#open the catalogue/fits
cat=fits.open(catalogue)
img=fits.open(image)
seg=fits.open(segmap)
det=fits.open(detection)
#grab reference wcs from detection image
try:
wref=wcs.WCS(det[1].header)
except:
wref = wcs.WCS(det[0].header)
psref=wref.pixel_scale_matrix[1,1]*3600.
print ('Reference pixel size {}'.format(psref))
#if not handling MUSE, special cases for format of data
if('MUSE' not in instrument):
#handle instrument cases
if('LRIS' in instrument):
#data
imgdata=img[1].data
#place holder for varaince as will use noise model below
vardata=imgdata*0+1
vardata=vardata.byteswap(True).newbyteorder()
#grab wcs image
wimg=wcs.WCS(img[1].header)
psimg=wimg.pixel_scale_matrix[1,1]*3600.
#store the ZP
if(zpab):
img[0].header['ZPAB']=zpab
else:
print('Instrument not supported!!')
exit()
else:
#for muse, keep eveything the same
imgdata=img[0].data
vardata=img[1].data
psimg=psref
#grab flux and var
dataflx=np.nan_to_num(imgdata.byteswap(True).newbyteorder())
datavar=np.nan_to_num(vardata.byteswap(True).newbyteorder())
# import pdb; pdb.set_trace()
#grab detection and seg mask
try:
detflx=np.nan_to_num(det[1].data.byteswap(True).newbyteorder())
except:
detflx = np.nan_to_num(det[0].data.byteswap(True).newbyteorder())
#go back to 1d
if(len(seg[0].data.shape)>2):
segmask=(np.nan_to_num(seg[0].data.byteswap(True).newbyteorder()))[0,:,:]
else:
segmask=(np.nan_to_num(seg[0].data.byteswap(True).newbyteorder()))
#if needed, map the segmap to new image with transformation
if('MUSE' not in instrument):
#allocate space for transformed segmentation map
segmasktrans=np.zeros(dataflx.shape)
print("Remapping segmentation map to new image...")
#loop over original segmap and map to trasformed one
#Just use nearest pixel, and keep only 1 when multiple choices
for xx in range(segmask.shape[0]):
for yy in range(segmask.shape[1]):
#go to world
radec=wref.wcs_pix2world([[yy,xx]],0)
#back to new instrument pixel
newxy=wimg.wcs_world2pix(radec,0)
#apply shift to register WCS
newxy[0][1]=newxy[0][1]+dyp
newxy[0][0]=newxy[0][0]+dxp
segmasktrans[newxy[0][1],newxy[0][0]]=segmask[xx,yy]
#grow buffer as needed by individual instruments
#This accounts for resampling to finer pixel size
if('LRIS' in instrument):
segmasktrans[newxy[0][1]+1,newxy[0][0]+1]=segmask[xx,yy]
segmasktrans[newxy[0][1]-1,newxy[0][0]-1]=segmask[xx,yy]
segmasktrans[newxy[0][1]+1,newxy[0][0]-1]=segmask[xx,yy]
segmasktrans[newxy[0][1]-1,newxy[0][0]+1]=segmask[xx,yy]
segmasktrans[newxy[0][1]+1,newxy[0][0]]=segmask[xx,yy]
segmasktrans[newxy[0][1]-1,newxy[0][0]]=segmask[xx,yy]
segmasktrans[newxy[0][1],newxy[0][0]-1]=segmask[xx,yy]
segmasktrans[newxy[0][1],newxy[0][0]+1]=segmask[xx,yy]
#dump the transformed segmap for checking
hdumain = fits.PrimaryHDU(segmasktrans,header=img[1].header)
hdulist = fits.HDUList(hdumain)
hdulist.writeto("{}_segremap.fits".format(rname),clobber=True)
else:
#no transformation needed
segmasktrans=segmask
#source to extract
nsrc=len(cat[1].data)
print('Extract photometry for {} sources'.format(nsrc))
phot = Table(names=('ID', 'MAGAP', 'MAGAP_ERR','FXAP', 'FXAP_ERR',
'RAD', 'MAGSEG', 'MAGSEG_ERR', 'FXSEG', 'FXSEG_ERR','ZP'),
dtype=('i4','f4','f4','f4','f4','f4','f4','f4','f4','f4','f4'))
#create check aperture mask
checkaperture=np.zeros(dataflx.shape)
print('Computing photometry for objects...')
#loop over each source
for idobj in range(nsrc):
#########
#Find positions etc and transform as appropriate
#########
#extract MUSE source paramaters
x= cat[1].data['x'][idobj]
y= cat[1].data['y'][idobj]
a= cat[1].data['a'][idobj]
b= cat[1].data['b'][idobj]
theta= cat[1].data['theta'][idobj]
#compute kron radius on MUSE detection image
#Kron rad in units of a,b
tmpdata=np.copy(detflx)
tmpmask=np.copy(segmask)
#mask all other sources to avoid overlaps but keep desired one
pixels=np.where(tmpmask == idobj+1)
tmpmask[pixels]=0
#compute kron radius [pixel of reference image]
kronrad, flg = sep.kron_radius(tmpdata,x,y,a,b,theta,6.0,mask=tmpmask)
#plt.imshow(np.log10(tmpdata+1),origin='low')
#plt.show()
#exit()
#now check if size is sensible in units of MUSE data
rmin = 2.0 #MUSE pix
use_circle = kronrad * np.sqrt(a*b) < rmin
#use circular aperture of 2" in muse pixel unit
rcircap = circap/psref
#now use info to compute photometry and apply
#spatial transformation if needed
if('MUSE' not in instrument):
#map centre of aperture - +1 reference
#go to world
radec=wref.wcs_pix2world([[x,y]],1)
#back to new instrument pixel
newxy=wimg.wcs_world2pix(radec,1)
#apply shift to register WCS
xphot=newxy[0][0]+dxp
yphot=newxy[0][1]+dyp
#scale radii to new pixel size
rminphot=rcircap*psref/psimg
aphot=a*psref/psimg
bphot=b*psref/psimg
#Kron radius in units of a,b
else:
#for muse, transfer to same units
xphot=x
yphot=y
rminphot=rcircap
aphot=a
bphot=b
#####
#Compute local sky
#####
skyreg=kn*kronrad*np.sqrt(aphot*bphot)+15
if (yphot-skyreg < 0.0): yphot=skyreg
if (xphot-skyreg < 0.0): xphot=skyreg
if (yphot+skyreg > segmasktrans.shape[0]-1): yphot=segmasktrans.shape[0]-1-skyreg
if (xphot+skyreg > segmasktrans.shape[1]-1): xphot=segmasktrans.shape[1]-1-skyreg
#print(int(yphot-skyreg),int(yphot+skyreg),int(xphot-skyreg),int(xphot+skyreg))
cutskymask=segmasktrans[int(yphot-skyreg):int(yphot+skyreg),int(xphot-skyreg):int(xphot+skyreg)]
cutskydata=dataflx[int(yphot-skyreg):int(yphot+skyreg),int(xphot-skyreg):int(xphot+skyreg)]
skymedian=np.nan_to_num(np.median(cutskydata[np.where(cutskymask < 1.0)]))
#print skymedian
#plt.imshow(cutskymask,origin='low')
#plt.show()
#if(idobj > 30):
# exit()
#########
#Now grab the Kron mag computed using detection image
#########
#mask all other objects to avoid blending
tmpdata=np.copy(dataflx)
#apply local sky subtraction
tmpdata=tmpdata-skymedian
tmpvar=np.copy(datavar)
tmpmask=np.copy(segmasktrans)
pixels=np.where(tmpmask == idobj+1)
tmpmask[pixels]=0
#plt.imshow(tmpmask,origin='low')
#plt.show()
#exit()
#circular aperture
if(use_circle):
#flux in circular aperture
flux_kron, err, flg = sep.sum_circle(tmpdata,xphot,yphot,rminphot,mask=tmpmask)
#propagate variance
fluxvar, err, flg = sep.sum_circle(tmpvar,xphot,yphot,rminphot,mask=tmpmask)
#store Rused in arcsec
rused=rminphot*psimg
#update check aperture
tmpcheckaper=np.zeros(dataflx.shape,dtype=bool)
sep.mask_ellipse(tmpcheckaper,xphot,yphot,1.,1.,0.,r=rminphot)
checkaperture=checkaperture+tmpcheckaper*(idobj+1)
#kron apertures
else:
#kron flux
flux_kron, err, flg = sep.sum_ellipse(tmpdata,xphot, yphot, aphot, bphot, theta, kn*kronrad,
mask=tmpmask)
#propagate variance
fluxvar, err, flg = sep.sum_ellipse(tmpvar,xphot,yphot, aphot, bphot, theta, kn*kronrad,
mask=tmpmask)
#translate in radius
rused=kn*kronrad*psimg*np.sqrt(aphot*bphot)
#update check aperture
tmpcheckaper=np.zeros(dataflx.shape,dtype=bool)
sep.mask_ellipse(tmpcheckaper,xphot,yphot,aphot,bphot,theta,r=kn*kronrad)
checkaperture=checkaperture+tmpcheckaper*(idobj+1)
#compute error for aperture
if(noise[0]):
#use model
appix=np.where(tmpcheckaper > 0)
errflux_kron=noise[0]*noise[1]*len(appix[0])**noise[2]
else:
#propagate variance
errflux_kron=np.sqrt(fluxvar)
#go to mag
if(flux_kron > 0):
mag_aper=-2.5*np.log10(flux_kron)+img[0].header['ZPAB']
errmg_aper=2.5*np.log10(1.+errflux_kron/flux_kron)
else:
mag_aper=99.0
errmg_aper=99.0
#find out if non detections
if(errflux_kron >= flux_kron):
errmg_aper=9
mag_aper=-2.5*np.log10(2.*errflux_kron)+img[0].header['ZPAB']
#######
#grab the photometry in the segmentation map
#####
#This may not work well for other instruments
#if images are not well aligned
pixels=np.where(segmasktrans == idobj+1)
#add flux in pixels
tmpdata=np.copy(dataflx)
#apply sky sub
tmpdata=tmpdata-skymedian
flux_seg=np.sum(tmpdata[pixels])
#compute noise from model or adding variance
if(noise[0]):
#from model
errfx_seg=noise[0]*noise[1]*len(pixels[0])**noise[2]
else:
#add variance in pixels to compute error
errfx_seg=np.sqrt(np.sum(datavar[pixels]))
#go to mag with calibrations
if(flux_seg > 0):
mag_seg=-2.5*np.log10(flux_seg)+img[0].header['ZPAB']
errmg_seg=2.5*np.log10(1.+errfx_seg/flux_seg)
else:
mag_seg=99.0
errmg_seg=99.0
#find out if non detections
if(errfx_seg >= flux_seg):
errmg_seg=9
mag_seg=-2.5*np.log10(2.*errfx_seg)+img[0].header['ZPAB']
#stash by id
phot.add_row((idobj+1,mag_aper,errmg_aper,flux_kron,errflux_kron,rused,mag_seg,errmg_seg,
flux_seg,errfx_seg,img[0].header['ZPAB']))
#dump the aperture check image
hdumain = fits.PrimaryHDU(checkaperture,header=img[1].header)
hdulist = fits.HDUList(hdumain)
hdulist.writeto("{}_aper.fits".format(rname),clobber=True)
#close
cat.close()
img.close()
seg.close()
det.close()
return phot
def test_vs_sextractor():
"""Test behavior of sep versus sextractor.
Note: we turn deblending off for this test. This is because the
deblending algorithm uses a random number generator. Since the sequence
of random numbers is not the same between sextractor and sep or between
different platforms, object member pixels (and even the number of objects)
can differ when deblending is on.
Deblending is turned off by setting DEBLEND_MINCONT=1.0 in the sextractor
configuration file and by setting deblend_cont=1.0 in sep.extract().
"""
data = np.copy(image_data) # make an explicit copy so we can 'subfrom'
bkg = sep.Background(data, bw=64, bh=64, fw=3, fh=3)
# Test that SExtractor background is same as SEP:
bkgarr = bkg.back(dtype=np.float32)
assert_allclose(bkgarr, image_refback, rtol=1.e-5)
# Extract objects (use deblend_cont=1.0 to disable deblending).
bkg.subfrom(data)
objs = sep.extract(data, 1.5*bkg.globalrms, deblend_cont=1.0)
objs = np.sort(objs, order=['y'])
# Read SExtractor result
refobjs = np.loadtxt(IMAGECAT_FNAME, dtype=IMAGECAT_DTYPE)
refobjs = np.sort(refobjs, order=['y'])
# Found correct number of sources at the right locations?
assert_allclose(objs['x'], refobjs['x'] - 1., atol=1.e-3)
assert_allclose(objs['y'], refobjs['y'] - 1., atol=1.e-3)
# Test aperture flux
flux, fluxerr, flag = sep.sum_circle(data, objs['x'], objs['y'], 5.,
err=bkg.globalrms)
assert_allclose(flux, refobjs['flux_aper'], rtol=2.e-4)
assert_allclose(fluxerr, refobjs['fluxerr_aper'], rtol=1.0e-5)
# check if the flags work at all (comparison values
assert ((flag & sep.APER_TRUNC) != 0).sum() == 4
assert ((flag & sep.APER_HASMASKED) != 0).sum() == 0
# Test "flux_auto"
kr, flag = sep.kron_radius(data, objs['x'], objs['y'], objs['a'],
objs['b'], objs['theta'], 6.0)
flux, fluxerr, flag = sep.sum_ellipse(data, objs['x'], objs['y'],
objs['a'], objs['b'],
objs['theta'], r=2.5 * kr,
err=bkg.globalrms, subpix=1)
# For some reason, one object doesn't match. It's very small
# and kron_radius is set to 0.0 in SExtractor, but 0.08 in sep.
# Could be due to a change in SExtractor between v2.8.6 (used to
# generate "truth" catalog) and v2.18.11 (from which sep was forked).
i = 56 # index is 59 when deblending is on.
kr[i] = 0.0
flux[i] = 0.0
fluxerr[i] = 0.0
# We use atol for radius because it is reported to nearest 0.01 in
# reference objects.
assert_allclose(2.5*kr, refobjs['kron_radius'], atol=0.01, rtol=0.)
assert_allclose(flux, refobjs['flux_auto'], rtol=0.0005)
assert_allclose(fluxerr, refobjs['fluxerr_auto'], rtol=0.0005)
# Test ellipse representation conversion
cxx, cyy, cxy = sep.ellipse_coeffs(objs['a'], objs['b'], objs['theta'])
assert_allclose(cxx, objs['cxx'], rtol=1.e-4)
assert_allclose(cyy, objs['cyy'], rtol=1.e-4)
assert_allclose(cxy, objs['cxy'], rtol=1.e-4)
a, b, theta = sep.ellipse_axes(objs['cxx'], objs['cyy'], objs['cxy'])
assert_allclose(a, objs['a'], rtol=1.e-4)
assert_allclose(b, objs['b'], rtol=1.e-4)
assert_allclose(theta, objs['theta'], rtol=1.e-4)
#test round trip
cxx, cyy, cxy = sep.ellipse_coeffs(a, b, theta)
assert_allclose(cxx, objs['cxx'], rtol=1.e-4)
assert_allclose(cyy, objs['cyy'], rtol=1.e-4)
assert_allclose(cxy, objs['cxy'], rtol=1.e-4)
# test flux_radius
fr, flags = sep.flux_radius(data, objs['x'], objs['y'], 6.*refobjs['a'],
[0.1, 0.5, 0.6], normflux=refobjs['flux_auto'],
subpix=5)
assert_allclose(fr, refobjs["flux_radius"], rtol=0.04, atol=0.01)
# test winpos
sig = 2. / 2.35 * fr[:, 1] # flux_radius = 0.5
xwin, ywin, flag = sep.winpos(data, objs['x'], objs['y'], sig)
assert_allclose(xwin, refobjs["xwin"] - 1., rtol=0., atol=0.0025)
assert_allclose(ywin, refobjs["ywin"] - 1., rtol=0., atol=0.0025)
def sourcephot(catalogue,image,segmap,detection,instrument='MUSE',dxp=0.,dyp=0.,
noise=[False],zpab=False, kn=2.5, circap=1.0):
"""
Get a source catalogue from findsources and a fits image with ZP
and compute magnitudes in that filter
catalogue -> source cat from findsources
image -> fits image with ZP in header
segmap -> fits of segmentation map
detection -> the detection image, used to compute Kron radius
instrument -> if not MUSE, map positions from detection to image
dxp,dyp -> shifts in pixel of image to register MUSE and image astrometry
noise -> if set to a noise model, use equation noise[0]*noise[1]*npix**noise[2]
to compute the error
zpab -> if ZPAB (zeropoint AB) not stored in header, must be supplied
kn -> factor to be used when scaling Kron apertures [sextractor default 2.5]
circap -> radius in arcsec for aperture photmetry to be used when Kron aperture fails
"""
from astropy.io import fits
import numpy as np
import sep
import matplotlib.pyplot as plt
from astropy.table import Table
from astropy import wcs
#grab root name
rname=((image.split('/')[-1]).split('.fits'))[0]
print ('Working on {}'.format(rname))
#open the catalogue/fits
cat=fits.open(catalogue)
img=fits.open(image)
seg=fits.open(segmap)
det=fits.open(detection)
#grab reference wcs from detection image
wref=wcs.WCS(det[0].header)
psref=wref.pixel_scale_matrix[1,1]*3600.
print ('Reference pixel size {}'.format(psref))
#if not handling MUSE, special cases for format of data
if('MUSE' not in instrument):
#handle instrument cases
if('LRIS' in instrument):
#data
imgdata=img[1].data
#place holder for varaince as will use noise model below
vardata=imgdata*0+1
vardata=vardata.byteswap(True).newbyteorder()
#grab wcs image
wimg=wcs.WCS(img[1].header)
psimg=wimg.pixel_scale_matrix[1,1]*3600.
#store the ZP
if(zpab):
img[0].header['ZPAB']=zpab
else:
print 'Instrument not supported!!'
exit()
else:
#for muse, keep eveything the same
imgdata=img[0].data
vardata=img[1].data
psimg=psref
#grab flux and var
dataflx=np.nan_to_num(imgdata.byteswap(True).newbyteorder())
datavar=np.nan_to_num(vardata.byteswap(True).newbyteorder())
#grab detection and seg mask
detflx=np.nan_to_num(det[0].data.byteswap(True).newbyteorder())
#go back to 1d
segmask=(np.nan_to_num(seg[0].data.byteswap(True).newbyteorder()))[0,:,:]
#if needed, map the segmap to new image with transformation
if('MUSE' not in instrument):
#allocate space for transformed segmentation map
segmasktrans=np.zeros(dataflx.shape)
print "Remapping segmentation map to new image..."
#loop over original segmap and map to trasformed one
#Just use nearest pixel, and keep only 1 when multiple choices
for xx in range(segmask.shape[0]):
for yy in range(segmask.shape[1]):
#go to world
radec=wref.wcs_pix2world([[yy,xx]],0)
#back to new instrument pixel
newxy=wimg.wcs_world2pix(radec,0)
#apply shift to register WCS
newxy[0][1]=newxy[0][1]+dyp
newxy[0][0]=newxy[0][0]+dxp
segmasktrans[newxy[0][1],newxy[0][0]]=segmask[xx,yy]
#grow buffer as needed by individual instruments
#This accounts for resampling to finer pixel size
if('LRIS' in instrument):
segmasktrans[newxy[0][1]+1,newxy[0][0]+1]=segmask[xx,yy]
segmasktrans[newxy[0][1]-1,newxy[0][0]-1]=segmask[xx,yy]
segmasktrans[newxy[0][1]+1,newxy[0][0]-1]=segmask[xx,yy]
segmasktrans[newxy[0][1]-1,newxy[0][0]+1]=segmask[xx,yy]
segmasktrans[newxy[0][1]+1,newxy[0][0]]=segmask[xx,yy]
segmasktrans[newxy[0][1]-1,newxy[0][0]]=segmask[xx,yy]
segmasktrans[newxy[0][1],newxy[0][0]-1]=segmask[xx,yy]
segmasktrans[newxy[0][1],newxy[0][0]+1]=segmask[xx,yy]
#dump the transformed segmap for checking
hdumain = fits.PrimaryHDU(segmasktrans,header=img[1].header)
hdulist = fits.HDUList(hdumain)
hdulist.writeto("{}_segremap.fits".format(rname),clobber=True)
else:
#no transformation needed
segmasktrans=segmask
#source to extract
nsrc=len(cat[1].data)
print('Extract photometry for {} sources'.format(nsrc))
phot = Table(names=('ID', 'MAGAP', 'MAGAP_ERR','FXAP', 'FXAP_ERR',
'RAD', 'MAGSEG', 'MAGSEG_ERR', 'FXSEG', 'FXSEG_ERR','ZP'),
dtype=('i4','f4','f4','f4','f4','f4','f4','f4','f4','f4','f4'))
#create check aperture mask
checkaperture=np.zeros(dataflx.shape)
print('Computing photometry for objects...')
#loop over each source
for idobj in range(nsrc):
#########
#Find positions etc and transform as appropriate
#########
#extract MUSE source paramaters
x= cat[1].data['x'][idobj]
y= cat[1].data['y'][idobj]
a= cat[1].data['a'][idobj]
b= cat[1].data['b'][idobj]
theta= cat[1].data['theta'][idobj]
#compute kron radius on MUSE detection image
#Kron rad in units of a,b
tmpdata=np.copy(detflx)
tmpmask=np.copy(segmask)
#mask all other sources to avoid overlaps but keep desired one
pixels=np.where(tmpmask == idobj+1)
tmpmask[pixels]=0
#compute kron radius [pixel of reference image]
kronrad, flg = sep.kron_radius(tmpdata,x,y,a,b,theta,6.0,mask=tmpmask)
#plt.imshow(np.log10(tmpdata+1),origin='low')
#plt.show()
#exit()
#now check if size is sensible in units of MUSE data
rmin = 2.0 #MUSE pix
use_circle = kronrad * np.sqrt(a*b) < rmin
#use circular aperture of 2" in muse pixel unit
rcircap = circap/psref
#now use info to compute photometry and apply
#spatial transformation if needed
if('MUSE' not in instrument):
#map centre of aperture - +1 reference
#go to world
radec=wref.wcs_pix2world([[x,y]],1)
#back to new instrument pixel
newxy=wimg.wcs_world2pix(radec,1)
#apply shift to register WCS
xphot=newxy[0][0]+dxp
yphot=newxy[0][1]+dyp
#scale radii to new pixel size
rminphot=rcircap*psref/psimg
aphot=a*psref/psimg
bphot=b*psref/psimg
#Kron radius in units of a,b
else:
#for muse, transfer to same units
xphot=x
yphot=y
rminphot=rcircap
aphot=a
bphot=b
#####
#Compute local sky
#####
skyreg=kn*kronrad*np.sqrt(aphot*bphot)+15
cutskymask=segmasktrans[yphot-skyreg:yphot+skyreg,xphot-skyreg:xphot+skyreg]
cutskydata=dataflx[yphot-skyreg:yphot+skyreg,xphot-skyreg:xphot+skyreg]
skymedian=np.nan_to_num(np.median(cutskydata[np.where(cutskymask < 1.0)]))
#print skymedian
#plt.imshow(cutskymask,origin='low')
#plt.show()
#if(idobj > 30):
# exit()
#########
#Now grab the Kron mag computed using detection image
#########
#mask all other objects to avoid blending
tmpdata=np.copy(dataflx)
#apply local sky subtraction
tmpdata=tmpdata-skymedian
tmpvar=np.copy(datavar)
tmpmask=np.copy(segmasktrans)
pixels=np.where(tmpmask == idobj+1)
tmpmask[pixels]=0
#plt.imshow(tmpmask,origin='low')
#plt.show()
#exit()
#circular aperture
if(use_circle):
#flux in circular aperture
flux_kron, err, flg = sep.sum_circle(tmpdata,xphot,yphot,rminphot,mask=tmpmask)
#propagate variance
fluxvar, err, flg = sep.sum_circle(tmpvar,xphot,yphot,rminphot,mask=tmpmask)
#store Rused in arcsec
rused=rminphot*psimg
#update check aperture
tmpcheckaper=np.zeros(dataflx.shape,dtype=bool)
sep.mask_ellipse(tmpcheckaper,xphot,yphot,1.,1.,0.,r=rminphot)
checkaperture=checkaperture+tmpcheckaper*(idobj+1)
#kron apertures
else:
#kron flux
flux_kron, err, flg = sep.sum_ellipse(tmpdata,xphot, yphot, aphot, bphot, theta, kn*kronrad,
mask=tmpmask)
#propagate variance
fluxvar, err, flg = sep.sum_ellipse(tmpvar,xphot,yphot, aphot, bphot, theta, kn*kronrad,
mask=tmpmask)
#translate in radius
rused=kn*kronrad*psimg*np.sqrt(aphot*bphot)
#update check aperture
tmpcheckaper=np.zeros(dataflx.shape,dtype=bool)
sep.mask_ellipse(tmpcheckaper,xphot,yphot,aphot,bphot,theta,r=kn*kronrad)
checkaperture=checkaperture+tmpcheckaper*(idobj+1)
#compute error for aperture
if(noise[0]):
#use model
appix=np.where(tmpcheckaper > 0)
errflux_kron=noise[0]*noise[1]*len(appix[0])**noise[2]
else:
#propagate variance
errflux_kron=np.sqrt(fluxvar)
#go to mag
if(flux_kron > 0):
mag_aper=-2.5*np.log10(flux_kron)+img[0].header['ZPAB']
errmg_aper=2.5*np.log10(1.+errflux_kron/flux_kron)
else:
mag_aper=99.0
errmg_aper=99.0
#find out if non detections
if(errflux_kron >= flux_kron):
errmg_aper=9
mag_aper=-2.5*np.log10(2.*errflux_kron)+img[0].header['ZPAB']
#######
#grab the photometry in the segmentation map
#####
#This may not work well for other instruments
#if images are not well aligned
pixels=np.where(segmasktrans == idobj+1)
#add flux in pixels
tmpdata=np.copy(dataflx)
#apply sky sub
tmpdata=tmpdata-skymedian
flux_seg=np.sum(tmpdata[pixels])
#compute noise from model or adding variance
if(noise[0]):
#from model
errfx_seg=noise[0]*noise[1]*len(pixels[0])**noise[2]
else:
#add variance in pixels to compute error
errfx_seg=np.sqrt(np.sum(datavar[pixels]))
#go to mag with calibrations
if(flux_seg > 0):
mag_seg=-2.5*np.log10(flux_seg)+img[0].header['ZPAB']
errmg_seg=2.5*np.log10(1.+errfx_seg/flux_seg)
else:
mag_seg=99.0
errmg_seg=99.0
#find out if non detections
if(errfx_seg >= flux_seg):
errmg_seg=9
mag_seg=-2.5*np.log10(2.*errfx_seg)+img[0].header['ZPAB']
#stash by id
phot.add_row((idobj+1,mag_aper,errmg_aper,flux_kron,errflux_kron,rused,mag_seg,errmg_seg,
flux_seg,errfx_seg,img[0].header['ZPAB']))
#dump the aperture check image
hdumain = fits.PrimaryHDU(checkaperture,header=img[1].header)
hdulist = fits.HDUList(hdumain)
hdulist.writeto("{}_aper.fits".format(rname),clobber=True)
#close
cat.close()
img.close()
seg.close()
det.close()
return phot
def get_hostgalaxy_params(self, scaleup=2.5):
'''
Gives x, y, a, b, theta of host galaxy
determined to be the object with smallest DLR from target
'''
if not hasattr(self, "hg_ellipse"):
raise AttributeError(
"No host galaxy detected yet. " +
"Run self.get_hostgalaxy() or set self.hg_ellipse")
self.var_count = {
band: self.target.imgcutout[band].weightimage.data**(-2)
for band in self.bands
}
counts_res = {
band: sep.sum_ellipse(self.cutout[band].data,
self.hg_ellipse[0],
self.hg_ellipse[1],
2 * self.hg_ellipse[2] * scaleup,
2 * self.hg_ellipse[3] * scaleup,
self.hg_ellipse[4],
var=self.var_count[band])
for band in self.bands
}
self.hg_count = {
band: [counts_res[band][0], counts_res[band][1]]
for band in self.bands
}
self.hg_flux = {
band: [
self.count_to_flux(self.hg_count[band][0]),
self.count_to_flux(self.hg_count[band][1])
]
for band in self.bands
}
self.var_flux = {
band: self.hg_flux[band][-1]**2
for band in self.bands
}
self.hg_mag = {
band: np.array(
flux_to_mag(self.hg_flux[band][0],
self.hg_flux[band][1],
zp=ps1_zp[band]))
for band in self.bands
}
phtpt = {
band: get_photopoint(self.hg_flux[band][0],
self.var_flux[band],
lbda=PANSTARRS_INFO[band]['lbda'],
bandname=PANSTARRS_INFO[band]['band'])
for band in ['g', 'i']
}
MassEstimate_obj = get_massestimator(
photopoints=[phtpt['g'], phtpt['i']])
MassEstimate_obj.set_target(get_target(zcmb=self.z))
self.hg_mass = MassEstimate_obj.get_estimate()
return self.hg_mass
def do_stage(self, images):
for i, image in enumerate(images):
try:
# Set the number of source pixels to be 5% of the total. This keeps us safe from
# satellites and airplanes.
sep.set_extract_pixstack(int(image.nx * image.ny * 0.05))
data = image.data.copy()
error = (np.abs(data) + image.readnoise ** 2.0) ** 0.5
mask = image.bpm > 0
# Fits can be backwards byte order, so fix that if need be and subtract
# the background
try:
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
except ValueError:
data = data.byteswap(True).newbyteorder()
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
bkg.subfrom(data)
# Do an initial source detection
# TODO: Add back in masking after we are sure SEP works
sources = sep.extract(data, self.threshold, minarea=self.min_area,
err=error, deblend_cont=0.005)
# Convert the detections into a table
sources = Table(sources)
# Calculate the ellipticity
sources['ellipticity'] = 1.0 - (sources['b'] / sources['a'])
# Fix any value of theta that are invalid due to floating point rounding
# -pi / 2 < theta < pi / 2
sources['theta'][sources['theta'] > (np.pi / 2.0)] -= np.pi
sources['theta'][sources['theta'] < (-np.pi / 2.0)] += np.pi
# Calculate the kron radius
kronrad, krflag = sep.kron_radius(data, sources['x'], sources['y'],
sources['a'], sources['b'],
sources['theta'], 6.0)
sources['flag'] |= krflag
sources['kronrad'] = kronrad
# Calcuate the equivilent of flux_auto
flux, fluxerr, flag = sep.sum_ellipse(data, sources['x'], sources['y'],
sources['a'], sources['b'],
np.pi / 2.0, 2.5 * kronrad,
subpix=1, err=error)
sources['flux'] = flux
sources['fluxerr'] = fluxerr
sources['flag'] |= flag
# Calculate the FWHMs of the stars:
fwhm = 2.0 * (np.log(2) * (sources['a'] ** 2.0 + sources['b'] ** 2.0)) ** 0.5
sources['fwhm'] = fwhm
# Cut individual bright pixels. Often cosmic rays
sources = sources[fwhm > 1.0]
# Measure the flux profile
flux_radii, flag = sep.flux_radius(data, sources['x'], sources['y'],
6.0 * sources['a'], [0.25, 0.5, 0.75],
normflux=sources['flux'], subpix=5)
sources['flag'] |= flag
sources['fluxrad25'] = flux_radii[:, 0]
sources['fluxrad50'] = flux_radii[:, 1]
sources['fluxrad75'] = flux_radii[:, 2]
# Calculate the windowed positions
sig = 2.0 / 2.35 * sources['fluxrad50']
xwin, ywin, flag = sep.winpos(data, sources['x'], sources['y'], sig)
sources['flag'] |= flag
sources['xwin'] = xwin
sources['ywin'] = ywin
# Calculate the average background at each source
bkgflux, fluxerr, flag = sep.sum_ellipse(bkg.back(), sources['x'], sources['y'],
sources['a'], sources['b'], np.pi / 2.0,
2.5 * sources['kronrad'], subpix=1)
#masksum, fluxerr, flag = sep.sum_ellipse(mask, sources['x'], sources['y'],
# sources['a'], sources['b'], np.pi / 2.0,
# 2.5 * kronrad, subpix=1)
background_area = (2.5 * sources['kronrad']) ** 2.0 * sources['a'] * sources['b'] * np.pi # - masksum
sources['background'] = bkgflux
sources['background'][background_area > 0] /= background_area[background_area > 0]
# Update the catalog to match fits convention instead of python array convention
sources['x'] += 1.0
sources['y'] += 1.0
sources['xpeak'] += 1
sources['ypeak'] += 1
sources['xwin'] += 1.0
sources['ywin'] += 1.0
sources['theta'] = np.degrees(sources['theta'])
image.catalog = sources['x', 'y', 'xwin', 'ywin', 'xpeak', 'ypeak',
'flux', 'fluxerr', 'background', 'fwhm',
'a', 'b', 'theta', 'kronrad', 'ellipticity',
'fluxrad25', 'fluxrad50', 'fluxrad75',
'x2', 'y2', 'xy', 'flag']
# Add the units and description to the catalogs
image.catalog['x'].unit = 'pixel'
image.catalog['x'].description = 'X coordinate of the object'
image.catalog['y'].unit = 'pixel'
image.catalog['y'].description = 'Y coordinate of the object'
image.catalog['xwin'].unit = 'pixel'
image.catalog['xwin'].description = 'Windowed X coordinate of the object'
image.catalog['ywin'].unit = 'pixel'
image.catalog['ywin'].description = 'Windowed Y coordinate of the object'
image.catalog['xpeak'].unit = 'pixel'
image.catalog['xpeak'].description = 'X coordinate of the peak'
image.catalog['ypeak'].unit = 'pixel'
image.catalog['ypeak'].description = 'Windowed Y coordinate of the peak'
image.catalog['flux'].unit = 'counts'
image.catalog['flux'].description = 'Flux within a Kron-like elliptical aperture'
image.catalog['fluxerr'].unit = 'counts'
image.catalog['fluxerr'].description = 'Erronr on the flux within a Kron-like elliptical aperture'
image.catalog['background'].unit = 'counts'
image.catalog['background'].description = 'Average background value in the aperture'
image.catalog['fwhm'].unit = 'pixel'
image.catalog['fwhm'].description = 'FWHM of the object'
image.catalog['a'].unit = 'pixel'
image.catalog['a'].description = 'Semi-major axis of the object'
image.catalog['b'].unit = 'pixel'
image.catalog['b'].description = 'Semi-minor axis of the object'
image.catalog['theta'].unit = 'degrees'
image.catalog['theta'].description = 'Position angle of the object'
image.catalog['kronrad'].unit = 'pixel'
image.catalog['kronrad'].description = 'Kron radius used for extraction'
image.catalog['ellipticity'].description = 'Ellipticity'
image.catalog['fluxrad25'].unit = 'pixel'
image.catalog['fluxrad25'].description = 'Radius containing 25% of the flux'
image.catalog['fluxrad50'].unit = 'pixel'
image.catalog['fluxrad50'].description = 'Radius containing 50% of the flux'
image.catalog['fluxrad75'].unit = 'pixel'
image.catalog['fluxrad75'].description = 'Radius containing 75% of the flux'
image.catalog['x2'].unit = 'pixel^2'
image.catalog['x2'].description = 'Variance on X coordinate of the object'
image.catalog['y2'].unit = 'pixel^2'
image.catalog['y2'].description = 'Variance on Y coordinate of the object'
image.catalog['xy'].unit = 'pixel^2'
image.catalog['xy'].description = 'XY covariance of the object'
image.catalog['flag'].description = 'Bit mask combination of extraction and photometry flags'
image.catalog.sort('flux')
image.catalog.reverse()
logging_tags = logs.image_config_to_tags(image, self.group_by_keywords)
logs.add_tag(logging_tags, 'filename', os.path.basename(image.filename))
# Save some background statistics in the header
mean_background = stats.sigma_clipped_mean(bkg.back(), 5.0)
image.header['L1MEAN'] = (mean_background,
'[counts] Sigma clipped mean of frame background')
logs.add_tag(logging_tags, 'L1MEAN', float(mean_background))
median_background = np.median(bkg.back())
image.header['L1MEDIAN'] = (median_background,
'[counts] Median of frame background')
logs.add_tag(logging_tags, 'L1MEDIAN', float(median_background))
std_background = stats.robust_standard_deviation(bkg.back())
image.header['L1SIGMA'] = (std_background,
'[counts] Robust std dev of frame background')
logs.add_tag(logging_tags, 'L1SIGMA', float(std_background))
# Save some image statistics to the header
good_objects = image.catalog['flag'] == 0
seeing = np.median(image.catalog['fwhm'][good_objects]) * image.pixel_scale
image.header['L1FWHM'] = (seeing, '[arcsec] Frame FWHM in arcsec')
logs.add_tag(logging_tags, 'L1FWHM', float(seeing))
mean_ellipticity = stats.sigma_clipped_mean(sources['ellipticity'][good_objects],
3.0)
image.header['L1ELLIP'] = (mean_ellipticity, 'Mean image ellipticity (1-B/A)')
logs.add_tag(logging_tags, 'L1ELLIP', float(mean_ellipticity))
mean_position_angle = stats.sigma_clipped_mean(sources['theta'][good_objects], 3.0)
image.header['L1ELLIPA'] = (mean_position_angle,
'[deg] PA of mean image ellipticity')
logs.add_tag(logging_tags, 'L1ELLIPA', float(mean_position_angle))
self.logger.info('Extracted sources', extra=logging_tags)
except Exception as e:
logging_tags = logs.image_config_to_tags(image, self.group_by_keywords)
logs.add_tag(logging_tags, 'filename', os.path.basename(image.filename))
self.logger.error(e, extra=logging_tags)
return images
for i in range(len(objects)):
e = Ellipse(xy=(objects['x'][i], objects['y'][i]),
width=6*objects['a'][i],
height=6*objects['b'][i],
angle=objects['theta'][i] * 180. / np.pi)
e.set_facecolor('none')
e.set_edgecolor('red')
ax.add_artist(e)
theta=0
b =1
apertures = [2.5,3.4,5,7.5,10,15,20,30,50,70]
catalog = []
f = []
a =1
flux, fluxerr, flag = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[0],err=bkg.globalrms, gain=1.4)
flux1, fluxerr1, flag1 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[1],err=bkg.globalrms, gain=1.4)
flux2, fluxerr2, flag2 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[2],err=bkg.globalrms, gain=1.4)
flux3, fluxerr3, flag3 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[3],err=bkg.globalrms, gain=1.4)
flux4, fluxerr4, flag4 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[4],err=bkg.globalrms, gain=1.4)
flux5, fluxer5r, flag5 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[5],err=bkg.globalrms, gain=1.4)
flux6, fluxerr6, flag6 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[6],err=bkg.globalrms, gain=1.4)
flux7, fluxerr7, flag7 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[7],err=bkg.globalrms, gain=1.4)
flux8, fluxerr8, flag8 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[8],err=bkg.globalrms, gain=1.4)
flux9, fluxerr9, flag9 = sep.sum_ellipse(data_sub, objects['x'], objects['y'], a, b, theta,apertures[9],err=bkg.globalrms, gain=1.4)
r, flag = sep.flux_radius(data_sub, objects['x'], objects['y'],6.*objects['a'], 0.5, normflux=flux, subpix=5)
r1, flag1 = sep.flux_radius(data_sub, objects['x'], objects['y'],6.*objects['a'], 0.5, normflux=flux, subpix=5)
r2, flag2 = sep.flux_radius(data_sub, objects['x'], objects['y'], 6.*objects['a'],0.5, normflux=flux, subpix=5)
r3, flag3 = sep.flux_radius(data_sub, objects['x'], objects['y'],6.*objects['a'], 0.5, normflux=flux, subpix=5)
r4, flag4 = sep.flux_radius(data_sub, objects['x'], objects['y'],6.*objects['a'], 0.5, normflux=flux, subpix=5)
r5, flag5 = sep.flux_radius(data_sub, objects['x'], objects['y'],6.*objects['a'], 0.5, normflux=flux, subpix=5)
if not CONDENSED:
print(blankline)
naper = 1000
nloop = 1
a = 1.
b = 1.
theta = np.pi/4.
for r in r_list:
for subpix, method, label in subpix_list:
line = "| ellipses r={0:2d} {1:8s} |".format(int(r), label)
t0 = time.time()
flux, fluxerr, flag = sep.sum_ellipse(data, x, y, a, b, theta, r,
subpix=subpix)
t1 = time.time()
t_sep = (t1-t0) * 1.e6 / naper / nloop
line += " {0:7.2f} us/aper |".format(t_sep)
if HAVE_PHOTUTILS:
apertures = photutils.EllipticalAperture((x, y), a*r, b*r, theta)
t0 = time.time()
res = photutils.aperture_photometry(
data, apertures, method=method, subpixels=subpix)
t1 = time.time()
t_pu = (t1-t0) * 1.e6 / naper
line += " {0:7.2f} us/aper | {1:6.2f} |".format(t_pu, t_pu/t_sep)
print(line)
def test_masked_segmentation_measurements():
"""Test measurements with segmentation masking"""
NX = 100
data = np.zeros((NX*2,NX*2))
yp, xp = np.indices(data.shape)
####
# Make two 2D gaussians that slightly overlap
# width of the 2D objects
gsigma = 10.
# offset between two gaussians in sigmas
off = 4
for xy in [[NX,NX], [NX+off*gsigma, NX+off*gsigma]]:
R = np.sqrt((xp-xy[0])**2+(yp-xy[1])**2)
g_i = np.exp(-R**2/2/gsigma**2)
data += g_i
# Absolute total
total_exact = g_i.sum()
# Add some noise
rms = 0.02
np.random.seed(1)
data += np.random.normal(size=data.shape)*rms
# Run source detection
objs, segmap = sep.extract(data, thresh=1.2, err=rms, mask=None,
segmentation_map=True)
seg_id = np.arange(1, len(objs)+1, dtype=np.int32)
# Compute Kron/Auto parameters
x, y, a, b = objs['x'], objs['y'], objs['a'], objs['b']
theta = objs['theta']
kronrad, krflag = sep.kron_radius(data, x, y, a, b, theta, 6.0)
flux_auto, fluxerr, flag = sep.sum_ellipse(data, x, y, a, b, theta,
2.5*kronrad,
segmap=segmap, seg_id=seg_id,
subpix=1)
# Test total flux
assert_allclose(flux_auto, total_exact, rtol=5.e-2)
# Flux_radius
for flux_fraction in [0.2, 0.5]:
# Exact solution
rhalf_exact = np.sqrt(-np.log(1-flux_fraction)*gsigma**2*2)
# Masked measurement
flux_radius, flag = sep.flux_radius(data, x, y, 6.*a, flux_fraction,
seg_id=seg_id, segmap=segmap,
normflux=flux_auto, subpix=5)
# Test flux fraction
assert_allclose(flux_radius, rhalf_exact, rtol=5.e-2)
if False:
print('test_masked_flux_radius')
print(total_exact, flux_auto)
print(rhalf_exact, flux_radius)
