def aper_phot(self,x,y):
"""Perform aperture photometry, uses photutils functions
Rapert, sum, area and flux are the radius of the aperture in
pixels, the total number of counts including sky in the aperture,
the area of the aperture in square pixels, and the total number of
counts in the aperture excluding sky. Mag and merr are the
magnitude and error in the magnitude in the aperture (see below).
flux = sum - area * msky
mag = zmag - 2.5 * log10 (flux) + 2.5 * log10 (itime)
merr = 1.0857 * error / flux
error = sqrt (flux / epadu + area * stdev**2 +
area**2 * stdev**2 / nsky)
"""
sigma=0. #no centering
amp=0. #no centering
if self.aperphot_pars["center"][0]:
center=True
delta=10
popt=self.gauss_center(x,y,delta)
if 5 > popt.count(0) > 1: #an error occurred in centering
warnings.warn("Problem fitting center, using original coordinates")
else:
amp,x,y,sigma,offset=popt
radius=int(self.aperphot_pars["radius"][0])
width=int(self.aperphot_pars["width"][0])
inner=int(self.aperphot_pars["skyrad"][0])
subsky=bool(self.aperphot_pars["subsky"][0])
aper_flux=photutils.aperture_photometry(self._data,x,y,apertures=photutils.CircularAperture(radius),subpixels=1,method="center")
aperture_area = np.pi * (radius)**2
if subsky:
outer=inner + width
annulus_sky=photutils.annulus_circular(self._data,x,y,inner,outer)
annulus_area = np.pi * (outer**2 - inner**2)
total_flux=aper_flux - annulus_sky * (aperture_area / annulus_area)
else:
total_flux=aper_flux
#compute the magnitude of the sky corrected flux
magzero=float(self.aperphot_pars["zmag"][0])
mag=magzero-2.5*(np.log10(total_flux))
pheader=("x\ty\tradius\tflux\tmag(zpt={0:0.2f})\tsky".format(magzero))
if center:
pheader+=("\tfwhm")
pstr="\n{0:.2f}\t{1:0.2f}\t{2:d}\t{3:0.2f}\t{4:0.2f}\t{5:0.2f}\t{6:0.2f}".format(x,y,radius,total_flux,mag,annulus_sky/annulus_area,math_helper.gfwhm(sigma))
else:
pstr="\n{0:0.2f}\t{1:0.2f}\t{2:d}\t{3:0.2f}\t{4:0.2f}\t{5:0.2f}".format(x,y,radius,total_flux,mag,annulus_sky/annulus_area,)
print(pheader+pstr)
logging.info(pheader + pstr)
def _aperture_phot(self,
x,
y,
radsize=1,
sky_inner=5,
skywidth=5,
method="subpixel",
subpixels=4):
"""Perform sky subtracted aperture photometry, uses photutils functions, photutil must be installed
Parameters
----------
radsize: int
Size of the radius
sky_inner: int
Inner radius of the sky annulus
skywidth: int
Width of the sky annulus
method: string
Pixel sampling method to use
subpixels: int
How many subpixels to use
Notes
-----
background is taken from sky annulus pixels, check into masking bad pixels
"""
if not photutils_installed:
print("Install photutils to enable")
else:
aper_flux = photutils.aperture_circular(self._data,
x,
y,
radsize,
subpixels=subpixels,
method=method)
aperture_area = np.pi * (radsize)**2
annulus_sky = photutils.annulus_circular(self._data, x, y,
sky_inner,
sky_inner + skywidth)
outer = sky_inner + skywidth
inner = sky_inner
annulus_area = np.pi * (outer**2 - inner**2)
skysub_flux = aper_flux - annulus_sky * (aperture_area /
annulus_area)
return (aper_flux, annulus_sky, skysub_flux)
def aper_phot(self, x, y):
"""Perform aperture photometry, uses photutils functions, photutils must be available
"""
if not photutils_installed:
print("Install photutil to enable")
else:
sigma = 0. # no centering
amp = 0. # no centering
if self.aperphot_pars["center"][0]:
center = True
delta = 10
popt = self.gauss_center(x, y, delta)
if 5 > popt.count(0) > 1: # an error occurred in centering
warnings.warn("Problem fitting center, using original coordinates")
else:
amp, x, y, sigma, offset = popt
radius = int(self.aperphot_pars["radius"][0])
width = int(self.aperphot_pars["width"][0])
inner = int(self.aperphot_pars["skyrad"][0])
subsky = bool(self.aperphot_pars["subsky"][0])
aper_flux = photutils.aperture_photometry(
self._data, x, y, apertures=photutils.CircularAperture(radius), subpixels=1, method="center")
aperture_area = np.pi * (radius) ** 2
if subsky:
outer = inner + width
annulus_sky = photutils.annulus_circular(self._data, x, y, inner, outer)
annulus_area = np.pi * (outer ** 2 - inner ** 2)
total_flux = aper_flux - annulus_sky * (aperture_area / annulus_area)
else:
total_flux = aper_flux
# compute the magnitude of the sky corrected flux
magzero = float(self.aperphot_pars["zmag"][0])
mag = magzero - 2.5 * (np.log10(total_flux))
pheader = (
"x\ty\tradius\tflux\tmag(zpt={0:0.2f})\tsky\t".format(magzero)).expandtabs(15)
if center:
pheader += ("fwhm")
pstr = "\n{0:.2f}\t{1:0.2f}\t{2:d}\t{3:0.2f}\t{4:0.2f}\t{5:0.2f}\t{6:0.2f}".format(
x + 1, y + 1, radius, total_flux, mag, annulus_sky / annulus_area, math_helper.gfwhm(sigma)).expandtabs(15)
else:
pstr = "\n{0:0.2f}\t{1:0.2f}\t{2:d}\t{3:0.2f}\t{4:0.2f}\t{5:0.2f}".format(
x + 1, y + 1, radius, total_flux, mag, annulus_sky / annulus_area,).expandtabs(15)
print(pheader + pstr)
logging.info(pheader + pstr)
def _aperture_phot(self,x,y,radsize=1,sky_inner=5,skywidth=5,method="subpixel",subpixels=4):
"""Perform sky subtracted aperture photometry, uses photutils functions
background is taken from sky annulus pixels, check into masking
"""
aper_flux=photutils.aperture_circular(self._data,x,y,radsize,subpixels=subpixels,method=method)
aperture_area = np.pi * (radsize)**2
annulus_sky=photutils.annulus_circular(self._data,x,y,sky_inner,sky_inner+skywidth)
outer=sky_inner+skywidth
inner=sky_inner
annulus_area = np.pi * (outer**2 - inner**2)
skysub_flux=aper_flux - annulus_sky * (aperture_area / annulus_area)
return (aper_flux,annulus_sky,skysub_flux)
def _aperture_phot(self, x, y, radsize=1, sky_inner=5, skywidth=5, method="subpixel", subpixels=4):
"""Perform sky subtracted aperture photometry, uses photutils functions, photutil must be installed
Parameters
----------
radsize: int
Size of the radius
sky_inner: int
Inner radius of the sky annulus
skywidth: int
Width of the sky annulus
method: string
Pixel sampling method to use
subpixels: int
How many subpixels to use
Notes
-----
background is taken from sky annulus pixels, check into masking bad pixels
"""
if not photutils_installed:
print("Install photutils to enable")
else:
aper_flux = photutils.aperture_circular(
self._data, x, y, radsize, subpixels=subpixels, method=method)
aperture_area = np.pi * (radsize) ** 2
annulus_sky = photutils.annulus_circular(
self._data, x, y, sky_inner, sky_inner + skywidth)
outer = sky_inner + skywidth
inner = sky_inner
annulus_area = np.pi * (outer ** 2 - inner ** 2)
skysub_flux = aper_flux - annulus_sky * (aperture_area / annulus_area)
return (aper_flux, annulus_sky, skysub_flux)
def aper_phot(self, x, y):
"""Perform aperture photometry, uses photutils functions, photutils must be available
"""
if not photutils_installed:
print("Install photutil to enable")
else:
sigma = 0. # no centering
amp = 0. # no centering
if self.aperphot_pars["center"][0]:
center = True
delta = 10
popt = self.gauss_center(x, y, delta)
if 5 > popt.count(0) > 1: # an error occurred in centering
warnings.warn(
"Problem fitting center, using original coordinates")
else:
amp, x, y, sigma, offset = popt
radius = int(self.aperphot_pars["radius"][0])
width = int(self.aperphot_pars["width"][0])
inner = int(self.aperphot_pars["skyrad"][0])
subsky = bool(self.aperphot_pars["subsky"][0])
aper_flux = photutils.aperture_photometry(
self._data,
x,
y,
apertures=photutils.CircularAperture(radius),
subpixels=1,
method="center")
aperture_area = np.pi * (radius)**2
if subsky:
outer = inner + width
annulus_sky = photutils.annulus_circular(
self._data, x, y, inner, outer)
annulus_area = np.pi * (outer**2 - inner**2)
total_flux = aper_flux - annulus_sky * (aperture_area /
annulus_area)
else:
total_flux = aper_flux
# compute the magnitude of the sky corrected flux
magzero = float(self.aperphot_pars["zmag"][0])
mag = magzero - 2.5 * (np.log10(total_flux))
pheader = ("x\ty\tradius\tflux\tmag(zpt={0:0.2f})\tsky\t".format(
magzero)).expandtabs(15)
if center:
pheader += ("fwhm")
pstr = "\n{0:.2f}\t{1:0.2f}\t{2:d}\t{3:0.2f}\t{4:0.2f}\t{5:0.2f}\t{6:0.2f}".format(
x + 1, y + 1, radius,
total_flux, mag, annulus_sky / annulus_area,
math_helper.gfwhm(sigma)).expandtabs(15)
else:
pstr = "\n{0:0.2f}\t{1:0.2f}\t{2:d}\t{3:0.2f}\t{4:0.2f}\t{5:0.2f}".format(
x + 1,
y + 1,
radius,
total_flux,
mag,
annulus_sky / annulus_area,
).expandtabs(15)
print(pheader + pstr)
logging.info(pheader + pstr)
def aperture(image, hdr):
global iap, pguess_old, nstars, svec
dnorm = 500.
rann1 = 18.
dann = 2.
rann2 = rann1 + dann
app_min = 1.
app_max = 19.
dapp = 1.
app_sizes = np.arange(app_min, app_max, dapp)
# If first time through, read in "guesses" for locations of stars
if iap == 0:
var = np.loadtxt('phot_coords')
xvec = var[:, 0]
yvec = var[:, 1]
nstars = len(xvec)
#print app_sizes,'\n'
else:
xvec = svec[:, 0]
yvec = svec[:, 1]
# Find locations of stars
dxx0 = 10.
for i in range(nstars):
xx0 = [xvec[i], yvec[i]]
xbounds = (xx0[0] - dxx0, xx0[0] + dxx0)
ybounds = (xx0[1] - dxx0, xx0[1] + dxx0)
#res = sco.minimize(center, xx0, method='BFGS', jac=der_center)
#res = sco.fmin_tnc(center, xx0, bounds=(xbounds,ybounds))
#res = sco.minimize(center, xx0, method='tnc', bounds=(xbounds,ybounds))
res = sco.minimize(center,
xx0,
method='L-BFGS-B',
bounds=(xbounds, ybounds),
jac=der_center)
xx0 = res.x
xvec[i] = xx0[0]
yvec[i] = xx0[1]
# Calculate sky around stars
sky = photutils.annulus_circular(image,
xvec,
yvec,
rann1,
rann2,
method='exact',
subpixels=10)
# Do psf fits to stars. Results are stored in arrays fwhm, pflux, psky, psf_x, and psf_y
fwhm = np.zeros(nstars)
# Make stacked array of star positions from aperture photometry
svec = np.dstack((xvec, yvec))[0]
#print svec
# Make stacked array of star positions from PSF fitting
# pvec = np.dstack((psf_x,psf_y))[0]
pvec = svec
iap = iap + 1
starr = []
apvec = []
app = -1.0
# Get time of observation from the header
#date = hdr['DATE-OBS'] # for Argos files
#utc = hdr['UTC'] # for Argos files
date = hdr['UTC-DATE'] # for Pro-EM files
utc = hdr['UTC-BEG'] # for Pro-EM files
times = date + " " + utc
t = Time(times, format='iso', scale='utc')
# Calculate Julian Date of observation
jd = t.jd
for app in app_sizes:
flux = photutils.aperture_circular(image,
xvec,
yvec,
app,
method='exact',
subpixels=10)
skyc = sky * app**2 / (rann2**2 - rann1**2)
fluxc = flux - skyc
starr.append([fluxc, skyc, fwhm])
apvec.append(app)
starr = np.array(starr)
apvec = np.array(apvec)
#print starr
return jd, svec, pvec, apvec, starr