def get_flux_and_err(imagedat, psfmodel, xy, ntestpositions=100, psfradpix=3,
apradpix=3, skyannpix=None, skyalgorithm='sigmaclipping',
setskyval=None, recenter_target=True, recenter_fakes=True,
exptime=1, exact=True, ronoise=1, phpadu=1, verbose=False,
debug=False):
""" Measure the flux and flux uncertainty for a source at the given x,y
position using both aperture and psf-fitting photometry.
Flux errors are measured by planting fake psfs or empty apertures into the
sky annulus and recovering a distribution of fluxes with forced photometry.
:param imagedat: target image numpy data array (with the star still there)
:param psfmodel: psf model fits file or a 4-tuple with
[gaussparam,lookuptable,psfmag,psfzpt]
:param xy: x,y position of the center of the fake planting field
:param ntestpositions: number of test positions for empty apertures
and/or fake stars to use for determining the flux error empirically.
:param psfradpix: radius to use for psf fitting, in pixels
:param apradpix: radius of photometry aperture, in pixels
:param skyannpix: inner and outer radius of sky annulus, in pixels
:param skyalgorithm: algorithm to use for determining the sky value from
the pixels within the sky annulus: 'sigmaclipping' or 'mmm'
:param setskyval: if not None, use this value for the sky, ignoring
the skyannulus
:param recenter_target: use cntrd to locate the target center near the
given xy position.
:param recenter_fakes: recenter on each planted fake when recovering it
:param exptime: exposure time of the image, for determining poisson noise
:param ronoise: read-out noise, for determining aperture flux error
analytically
:param phpadu: photons-per-ADU, for determining aper flux err analytically
:param verbose: turn verbosity on
:param debug: enter pdb debugging mode
:return: apflux, apfluxerr, psfflux, psffluxerr
The flux measured through the given aperture and through
psf fitting, along with associated errors.
"""
if not np.any(skyannpix):
skyannpix = [8, 15]
# locate the target star center position
x, y = xy
if recenter_target:
x, y = cntrd(imagedat, x, y, psfradpix)
if x < 0 or y < 0:
print("WARNING [photfunctions.py] : recentering failed")
import pdb
pdb.set_trace()
# do aperture photometry directly on the source
# (Note : using an arbitrary zeropoint of 25 here)
aperout = aper(imagedat, x, y, phpadu=phpadu,
apr=apradpix, skyrad=skyannpix,
setskyval=setskyval,
zeropoint=25, exact=exact,
verbose=verbose, skyalgorithm=skyalgorithm,
debug=debug)
apmag, apmagerr, apflux, apfluxerr, sky, skyerr, apbadflag, apoutstr = \
aperout
# define a set of test position points that uniformly samples the sky
# annulus region, for planting empty apertures and/or fake stars
rmin = float(skyannpix[0])
rmax = float(skyannpix[1])
u = np.random.uniform(rmin, rmax, ntestpositions)
v = np.random.uniform(0, rmin + rmax, ntestpositions)
r = np.where(v < u, u, rmax + rmin - u)
theta = np.random.uniform(0, 2 * np.pi, ntestpositions)
xtestpositions = r * np.cos(theta) + x
ytestpositions = r * np.sin(theta) + y
psfflux = psffluxerr = np.nan
if psfmodel is not None:
# set up the psf model realization
gaussparam, lookuptable, psfmag, psfzpt = rdpsfmodel(psfmodel)
psfmodel = [gaussparam, lookuptable, psfmag, psfzpt]
pk = pkfit_class(imagedat, gaussparam, lookuptable, ronoise, phpadu)
# do the psf fitting
try:
scale = pk.pkfit_fast_norecenter(1, x, y, sky, psfradpix)
psfflux = scale * 10 ** (0.4 * (25. - psfmag))
except RuntimeWarning:
print("PythonPhot.pkfit_norecenter failed.")
psfflux = np.nan
if np.isfinite(psfflux):
# remove the target star from the image
imagedat = addtoimarray(imagedat, psfmodel, [x, y],
fluxscale=-psfflux)
# plant fakes and recover their fluxes with psf fitting
# imdatsubarray = imagedat[y-rmax-2*psfradpix:y+rmax+2*psfradpix,
# x-rmax-2*psfradpix:x+rmax+2*psfradpix]
fakecoordlist, fakefluxlist = [], []
for xt, yt in zip(xtestpositions, ytestpositions):
# To ensure appropriate sampling of sub-pixel positions,
# we assign random sub-pixel offsets to each position.
xt = int(xt) + np.random.random()
yt = int(yt) + np.random.random()
fakefluxaper, fakefluxpsf, fakecoord = add_and_recover(
imagedat, psfmodel, [xt, yt], fluxscale=psfflux,
cleanup=True, psfradius=psfradpix, recenter=recenter_fakes)
if np.isfinite(fakefluxpsf):
fakecoordlist.append(fakecoord)
fakefluxlist.append(fakefluxpsf)
fakefluxlist = np.array(fakefluxlist)
fakefluxmean, fakefluxsigma = gaussian_fit_to_histogram(fakefluxlist)
if abs(fakefluxmean - psfflux) > fakefluxsigma and verbose:
print("WARNING: psf flux may be biased. Fake psf flux tests "
"found a significantly non-zero sky value not accounted for "
"in measurement of the target flux: \\"
"Mean psf flux offset in sky annulus = %.3e\\" %
(fakefluxmean - psfflux) +
"sigma of fake flux distribution = %.3e" %
fakefluxsigma +
"NOTE: this is included as a systematic error, added in "
"quadrature to the psf flux err derived from fake psf "
"recovery.")
psfflux_poissonerr = (poissonErr(psfflux * exptime, confidence=1) /
exptime)
# Total flux error is the quadratic sum of the poisson noise with
# the systematic (shift) and statistical (dispersion) errors
# inferred from fake psf planting and recovery
psffluxerr = np.sqrt(psfflux_poissonerr**2 +
(fakefluxmean - psfflux)**2 +
fakefluxsigma**2)
# drop down empty apertures and recover their fluxes with aperture phot
# NOTE : if the star was removed for psf fitting, then we take advantage
# of that to get aperture flux errors with the star gone.
emptyaperout = aper(imagedat, np.array(xtestpositions),
np.array(ytestpositions), phpadu=phpadu,
apr=apradpix, setskyval=sky, zeropoint=25,
exact=False, verbose=verbose,
skyalgorithm=skyalgorithm, debug=debug)
emptyapflux = emptyaperout[2]
if np.any(np.isfinite(emptyapflux)):
emptyapmeanflux, emptyapsigma = gaussian_fit_to_histogram(emptyapflux)
emptyapbias = abs(emptyapmeanflux) - emptyapsigma
if np.any(emptyapbias > 0) and verbose:
print("WARNING: aperture flux may be biased. Empty aperture flux tests"
" found a significantly non-zero sky value not accounted for in "
"measurement of the target flux: \\"
"Mean empty aperture flux in sky annulus = %s\\"
% emptyapmeanflux +
"sigma of empty aperture flux distribution = %s"
% emptyapsigma)
if np.iterable(apflux):
apflux_poissonerr = np.array(
[poissonErr(fap * exptime, confidence=1) / exptime
for fap in apflux])
else:
apflux_poissonerr = (poissonErr(apflux * exptime, confidence=1) /
exptime)
apfluxerr = np.sqrt(apflux_poissonerr**2 +
emptyapbias**2 + emptyapsigma**2)
else:
if np.iterable(apradpix):
apfluxerr = [np.nan for aprad in apradpix]
else:
apfluxerr = np.nan
if psfmodel is not None and np.isfinite(psfflux):
# return the target star back into the image
imagedat = addtoimarray(imagedat, psfmodel, [x, y],
fluxscale=psfflux)
if debug > 1:
import pdb
pdb.set_trace()
return apflux, apfluxerr, psfflux, psffluxerr, sky, skyerr
def add_and_recover(imagedat, psfmodel, xy, fluxscale=1, psfradius=5,
skyannpix=None, skyalgorithm='sigmaclipping',
setskyval=None, recenter=False, ronoise=1, phpadu=1,
cleanup=True, verbose=False, debug=False):
""" Add a single fake star psf model to the image at the given position
and flux scaling, re-measure the flux at that position and report it,
Also deletes the planted psf from the imagedat array so that we don't
pollute that image array.
:param imagedat: target image numpy data array
:param psfmodel: psf model fits file or tuple with [gaussparam,lookuptable]
:param xy: x,y position for fake psf, using the IDL/python convention
where [0,0] is the lower left corner.
:param fluxscale: flux scaling to apply to the planted psf
:param recenter: use cntrd to locate the center of the added psf, instead
of relying on the input x,y position to define the psf fitting
:param cleanup: remove the planted psf from the input imagedat array.
:return:
"""
if not skyannpix:
skyannpix = [8, 15]
# add the psf to the image data array
imdatwithpsf = addtoimarray(imagedat, psfmodel, xy, fluxscale=fluxscale)
# TODO: allow for uncertainty in the x,y positions
gaussparam, lookuptable, psfmag, psfzpt = rdpsfmodel(psfmodel)
# generate an instance of the pkfit class for this psf model
# and target image
pk = pkfit_class(imdatwithpsf, gaussparam, lookuptable, ronoise, phpadu)
x, y = xy
if debug:
from .photfunctions import showpkfit
from matplotlib import pyplot as pl, cm
fig = pl.figure(3)
showpkfit(imdatwithpsf, psfmodel, xy, 11, fluxscale, verbose=True)
fig = pl.figure(1)
pl.imshow(imdatwithpsf[y - 20:y + 20, x - 20:x + 20], cmap=cm.Greys,
interpolation='nearest')
pl.colorbar()
import pdb
pdb.set_trace()
if recenter:
xc, yc = cntrd(imdatwithpsf, x, y, psfradius, verbose=verbose)
if xc > 0 and yc > 0 and abs(xc - xy[0]) < 5 and abs(yc - xy[1]) < 5:
x, y = xc, yc
# do aperture photometry to get the sky
aperout = aper(imdatwithpsf, x, y, phpadu=phpadu,
apr=psfradius * 3, skyrad=skyannpix,
setskyval=(setskyval is not None and setskyval),
zeropoint=psfzpt, exact=False,
verbose=verbose, skyalgorithm=skyalgorithm,
debug=debug)
apmag, apmagerr, apflux, apfluxerr, sky, skyerr, apbadflag, apoutstr\
= aperout
# do the psf fitting
try:
scale = pk.pkfit_fast_norecenter(1, x, y, sky, psfradius)
fluxpsf = scale * 10 ** (-0.4 * (psfmag - psfzpt))
except RuntimeWarning:
print("photfunctions.add_and_recover failed on RuntimeWarning")
fluxpsf = -99
if cleanup:
# remove the fake psf from the image
imagedat = addtoimarray(imdatwithpsf, psfmodel, xy,
fluxscale=-fluxscale)
return apflux[0], fluxpsf, [x, y]