def snr_astropy(image,sx,sy,r,r_in,r_out):
"""
Returns signal to noise ratio, signal value, noise value using Astropy's Photutils module
Args:
image (2d float array): Image array extracted from fits file
sx,sy (float): x and y pixel locations for the center of the source
r (float): radius for aperture
r_in,r_out (float): inner and outer radii for annulus
Return:
snr (float): signal-to-noise ratio
signal (float): sum of all pixel values within the specified aperture minus sky background
noise (float): noise in the signal calculated as std deviation of pixels in the sky annulus times sqrt of the area of the
signal aperture
poisson_noise (float): snr determined from the poisson noise in the source signal. Poisson noise = sqrt(counts) [because variance
of a poisson distribution is the parameter itself]. Poisson snr = Signal/sqrt(signal) = sqrt(signal)
Written by: Logan Pearce, 2018
"""
import warnings
warnings.filterwarnings('ignore')
from photutils import CircularAperture, CircularAnnulus
positions = (cx-1,cy-1)
ap = CircularAperture(positions,r=r)
skyan = CircularAnnulus(positions,r_in=11,r_out=14)
apsum = ap.do_photometry(image)[0]
skysum = skyan.do_photometry(image)[0]
averagesky = skysum/skyan.area()
signal = (apsum - ap.area()*averagesky)[0]
n = ap.area()
ap_an = aperture_annulus(sx,sy,r,r_in,r_out)
skyan = ap_an[1]
poisson_noise = np.sqrt(signal)
noise = noise = np.std(image[skyan[1],skyan[0]])
noise = noise*np.sqrt(n)
snr = signal/noise
return snr,signal,noise,poisson_noise
def compute_snr(x, y):
positions = (x - 1, y - 1)
ap = CircularAperture(positions, r=radius)
skyan = CircularAnnulus(positions, r_in=11, r_out=14)
ap = CircularAperture(positions, r=radius)
skyan = CircularAnnulus(positions, r_in=11, r_out=14)
apsum = ap.do_photometry(image)[0]
skysum = skyan.do_photometry(image)[0]
averagesky = skysum / skyan.area()
signal = (apsum - ap.area() * averagesky)[0]
n = ap.area()
box = image[y + 12:y + 12 + 15, x + 12:x + 12 + 15]
noise = np.std(box)
noise = noise * np.sqrt(n)
snr = signal / noise
return snr
def tso_aperture_photometry(datamodel, xcenter, ycenter, radius, radius_inner,
radius_outer):
"""
Create a photometric catalog for NIRCam TSO imaging observations.
Parameters
----------
datamodel : `CubeModel`
The input `CubeModel` of a NIRCam TSO imaging observation.
xcenter, ycenter : float
The ``x`` and ``y`` center of the aperture.
radius : float
The radius (in pixels) of the circular aperture.
radius_inner, radius_outer : float
The inner and outer radii (in pixels) of the circular-annulus
aperture, used for local background estimation.
Returns
-------
catalog : `~astropy.table.QTable`
An astropy QTable (Quantity Table) containing the source
photometry.
"""
if not isinstance(datamodel, CubeModel):
raise ValueError('The input data model must be a CubeModel.')
# For the SUB64P subarray with the WLP8 pupil, the circular aperture
# extends beyond the image and the circular annulus does not have any
# overlap with the image. In that case, we simply sum all values
# in the array and skip the background subtraction.
sub64p_wlp8 = False
if (datamodel.meta.instrument.pupil == 'WLP8'
and datamodel.meta.subarray.name == 'SUB64P'):
sub64p_wlp8 = True
if not sub64p_wlp8:
phot_aper = CircularAperture((xcenter, ycenter), r=radius)
bkg_aper = CircularAnnulus((xcenter, ycenter),
r_in=radius_inner,
r_out=radius_outer)
# convert the input data and errors from MJy/sr to Jy
if datamodel.meta.bunit_data != 'MJy/sr':
raise ValueError('data is expected to be in units of MJy/sr')
factor = 1.e6 * datamodel.meta.photometry.pixelarea_steradians
datamodel.data *= factor
datamodel.err *= factor
datamodel.meta.bunit_data = 'Jy'
datamodel.meta.bunit_err = 'Jy'
aperture_sum = []
aperture_sum_err = []
annulus_sum = []
annulus_sum_err = []
nimg = datamodel.data.shape[0]
if sub64p_wlp8:
info = ('Photometry measured as the sum of all values in the '
'subarray. No background subtraction was performed.')
for i in np.arange(nimg):
aperture_sum.append(np.sum(datamodel.data[i, :, :]))
aperture_sum_err.append(np.sqrt(np.sum(datamodel.err[i, :, :]**2)))
else:
info = ('Photometry measured in a circular aperture of r={0} '
'pixels. Background calculated as the mean in a '
'circular annulus with r_inner={1} pixels and '
'r_outer={2} pixels.'.format(radius, radius_inner,
radius_outer))
for i in np.arange(nimg):
aper_sum, aper_sum_err = phot_aper.do_photometry(
datamodel.data[i, :, :], error=datamodel.err[i, :, :])
ann_sum, ann_sum_err = bkg_aper.do_photometry(
datamodel.data[i, :, :], error=datamodel.err[i, :, :])
aperture_sum.append(aper_sum[0])
aperture_sum_err.append(aper_sum_err[0])
annulus_sum.append(ann_sum[0])
annulus_sum_err.append(ann_sum_err[0])
aperture_sum = np.array(aperture_sum)
aperture_sum_err = np.array(aperture_sum_err)
annulus_sum = np.array(annulus_sum)
annulus_sum_err = np.array(annulus_sum_err)
# construct metadata for output table
meta = OrderedDict()
meta['instrument'] = datamodel.meta.instrument.name
meta['detector'] = datamodel.meta.instrument.detector
meta['channel'] = datamodel.meta.instrument.channel
meta['subarray'] = datamodel.meta.subarray.name
meta['filter'] = datamodel.meta.instrument.filter
meta['pupil'] = datamodel.meta.instrument.pupil
meta['target_name'] = datamodel.meta.target.catalog_name
meta['xcenter'] = xcenter
meta['ycenter'] = ycenter
ra_icrs, dec_icrs = datamodel.meta.wcs(xcenter, ycenter)
meta['ra_icrs'] = ra_icrs
meta['dec_icrs'] = dec_icrs
meta['apertures'] = info
# initialize the output table
tbl = QTable(meta=meta)
# check for the INT_TIMES table extension
if hasattr(datamodel, 'int_times') and datamodel.int_times is not None:
nrows = len(datamodel.int_times)
else:
nrows = 0
log.warning("The INT_TIMES table in the input file is missing or "
"empty.")
# load the INT_TIMES table data
if nrows > 0:
shape = datamodel.data.shape
if len(shape) == 2:
num_integ = 1
else: # len(shape) == 3
num_integ = shape[0]
int_start = datamodel.meta.exposure.integration_start
if int_start is None:
int_start = 1
log.warning(f"INTSTART not found; assuming a value of {int_start}")
# Columns of integration numbers & times of integration from the
# INT_TIMES table.
int_num = datamodel.int_times['integration_number']
mid_utc = datamodel.int_times['int_mid_MJD_UTC']
offset = int_start - int_num[0] # both are one-indexed
if offset < 0:
log.warning("Range of integration numbers in science data extends "
"outside the range in INT_TIMES table.")
log.warning("Can't use INT_TIMES table.")
del int_num, mid_utc
nrows = 0 # flag as bad
else:
log.debug("Times are from the INT_TIMES table")
time_arr = mid_utc[offset:offset + num_integ]
int_times = Time(time_arr, format='mjd', scale='utc')
# compute integration time stamps on the fly
if nrows == 0:
log.debug("Times computed from EXPSTART and EFFINTTM")
dt = datamodel.meta.exposure.integration_time
n_dt = (datamodel.meta.exposure.integration_end -
datamodel.meta.exposure.integration_start + 1)
dt_arr = (np.arange(1, 1 + n_dt) * dt - (dt / 2.))
int_dt = TimeDelta(dt_arr, format='sec')
int_times = (Time(datamodel.meta.exposure.start_time, format='mjd') +
int_dt)
# populate table columns
unit = u.Unit(datamodel.meta.bunit_data)
tbl['MJD'] = int_times.mjd
tbl['aperture_sum'] = aperture_sum << unit
tbl['aperture_sum_err'] = aperture_sum_err << unit
if not sub64p_wlp8:
tbl['annulus_sum'] = annulus_sum << unit
tbl['annulus_sum_err'] = annulus_sum_err << unit
if LooseVersion(photutils.__version__) >= '0.7':
annulus_mean = annulus_sum / bkg_aper.area
annulus_mean_err = annulus_sum_err / bkg_aper.area
aperture_bkg = annulus_mean * phot_aper.area
aperture_bkg_err = annulus_mean_err * phot_aper.area
else:
annulus_mean = annulus_sum / bkg_aper.area()
annulus_mean_err = annulus_sum_err / bkg_aper.area()
aperture_bkg = annulus_mean * phot_aper.area()
aperture_bkg_err = annulus_mean_err * phot_aper.area()
tbl['annulus_mean'] = annulus_mean << unit
tbl['annulus_mean_err'] = annulus_mean_err << unit
tbl['aperture_bkg'] = aperture_bkg << unit
tbl['aperture_bkg_err'] = aperture_bkg_err << unit
net_aperture_sum = aperture_sum - aperture_bkg
net_aperture_sum_err = np.sqrt(aperture_sum_err**2 +
aperture_bkg_err**2)
tbl['net_aperture_sum'] = net_aperture_sum << unit
tbl['net_aperture_sum_err'] = net_aperture_sum_err << unit
else:
colnames = [
'annulus_sum', 'annulus_sum_err', 'annulus_mean',
'annulus_mean_err', 'aperture_bkg', 'aperture_bkg_err'
]
for col in colnames:
tbl[col] = np.full(nimg, np.nan)
tbl['net_aperture_sum'] = aperture_sum << unit
tbl['net_aperture_sum_err'] = aperture_sum_err << unit
return tbl
def tso_aperture_photometry(datamodel, xcenter, ycenter, radius, radius_inner,
radius_outer):
"""
Create a photometric catalog for NIRCam TSO imaging observations.
Parameters
----------
datamodel : `CubeModel`
The input `CubeModel` of a NIRCam TSO imaging observation.
xcenter, ycenter : float
The ``x`` and ``y`` center of the aperture.
radius : float
The radius (in pixels) of the circular aperture.
radius_inner, radius_outer : float
The inner and outer radii (in pixels) of the circular-annulus
aperture, used for local background estimation.
Returns
-------
catalog : `~astropy.table.QTable`
An astropy QTable (Quantity Table) containing the source
photometry.
"""
if not isinstance(datamodel, CubeModel):
raise ValueError('The input data model must be a CubeModel.')
# For the SUB64P subarray with the WLP8 pupil, the circular aperture
# extends beyond the image and the circular annulus does not have any
# overlap with the image. In that case, we simply sum all values
# in the array and skip the background subtraction.
sub64p_wlp8 = False
if (datamodel.meta.instrument.pupil == 'WLP8' and
datamodel.meta.subarray.name == 'SUB64P'):
sub64p_wlp8 = True
if not sub64p_wlp8:
phot_aper = CircularAperture((xcenter, ycenter), r=radius)
bkg_aper = CircularAnnulus((xcenter, ycenter), r_in=radius_inner,
r_out=radius_outer)
aperture_sum = []
aperture_sum_err = []
annulus_sum = []
annulus_sum_err = []
nimg = datamodel.data.shape[0]
if sub64p_wlp8:
info = ('Photometry measured as the sum of all values in the '
'subarray. No background subtraction was performed.')
for i in np.arange(nimg):
aperture_sum.append(np.sum(datamodel.data[i, :, :]))
aperture_sum_err.append(
np.sqrt(np.sum(datamodel.err[i, :, :]**2)))
else:
info = ('Photometry measured in a circular aperture of r={0} '
'pixels. Background calculated as the mean in a '
'circular annulus with r_inner={1} pixels and '
'r_outer={2} pixels.'.format(radius, radius_inner,
radius_outer))
for i in np.arange(nimg):
aper_sum, aper_sum_err = phot_aper.do_photometry(
datamodel.data[i, :, :], error=datamodel.err[i, :, :])
ann_sum, ann_sum_err = bkg_aper.do_photometry(
datamodel.data[i, :, :], error=datamodel.err[i, :, :])
aperture_sum.append(aper_sum[0])
aperture_sum_err.append(aper_sum_err[0])
annulus_sum.append(ann_sum[0])
annulus_sum_err.append(ann_sum_err[0])
aperture_sum = np.array(aperture_sum)
aperture_sum_err = np.array(aperture_sum_err)
annulus_sum = np.array(annulus_sum)
annulus_sum_err = np.array(annulus_sum_err)
# construct metadata for output table
meta = OrderedDict()
meta['instrument'] = datamodel.meta.instrument.name
meta['detector'] = datamodel.meta.instrument.detector
meta['channel'] = datamodel.meta.instrument.channel
meta['subarray'] = datamodel.meta.subarray.name
meta['filter'] = datamodel.meta.instrument.filter
meta['pupil'] = datamodel.meta.instrument.pupil
meta['target_name'] = datamodel.meta.target.catalog_name
meta['xcenter'] = xcenter
meta['ycenter'] = ycenter
ra_icrs, dec_icrs = datamodel.meta.wcs(xcenter, ycenter)
meta['ra_icrs'] = ra_icrs
meta['dec_icrs'] = dec_icrs
meta['apertures'] = info
# initialize the output table
tbl = QTable(meta=meta)
if hasattr(datamodel, 'int_times') and datamodel.int_times is not None:
nrows = len(datamodel.int_times)
else:
nrows = 0
if nrows == 0:
log.warning("There is no INT_TIMES table in the input file.")
if nrows > 0:
shape = datamodel.data.shape
if len(shape) == 2:
num_integ = 1
else: # len(shape) == 3
num_integ = shape[0]
int_start = datamodel.meta.exposure.integration_start
if int_start is None:
int_start = 1
log.warning("INTSTART not found; assuming a value of %d",
int_start)
# Columns of integration numbers & times of integration from the
# INT_TIMES table.
int_num = datamodel.int_times['integration_number']
mid_utc = datamodel.int_times['int_mid_MJD_UTC']
offset = int_start - int_num[0] # both are one-indexed
if offset < 0:
log.warning("Range of integration numbers in science data extends "
"outside the range in INT_TIMES table.")
log.warning("Can't use INT_TIMES table.")
del int_num, mid_utc
nrows = 0 # flag as bad
else:
log.debug("Times are from the INT_TIMES table.")
time_arr = mid_utc[offset: offset + num_integ]
int_times = Time(time_arr, format='mjd', scale='utc')
else:
log.debug("Times were computed from EXPSTART and TGROUP.")
dt = (datamodel.meta.exposure.group_time *
(datamodel.meta.exposure.ngroups + 1))
dt_arr = (np.arange(1, 1 + datamodel.meta.exposure.nints) *
dt - (dt / 2.))
int_dt = TimeDelta(dt_arr, format='sec')
int_times = (Time(datamodel.meta.exposure.start_time, format='mjd') +
int_dt)
tbl['MJD'] = int_times.mjd
tbl['aperture_sum'] = aperture_sum
tbl['aperture_sum_err'] = aperture_sum_err
if not sub64p_wlp8:
tbl['annulus_sum'] = annulus_sum
tbl['annulus_sum_err'] = annulus_sum_err
annulus_mean = annulus_sum / bkg_aper.area()
annulus_mean_err = annulus_sum_err / bkg_aper.area()
tbl['annulus_mean'] = annulus_mean
tbl['annulus_mean_err'] = annulus_mean_err
aperture_bkg = annulus_mean * phot_aper.area()
aperture_bkg_err = annulus_mean_err * phot_aper.area()
tbl['aperture_bkg'] = aperture_bkg
tbl['aperture_bkg_err'] = aperture_bkg_err
net_aperture_sum = aperture_sum - aperture_bkg
net_aperture_sum_err = np.sqrt(aperture_sum_err ** 2 +
aperture_bkg_err ** 2)
tbl['net_aperture_sum'] = net_aperture_sum
tbl['net_aperture_sum_err'] = net_aperture_sum_err
else:
colnames = ['annulus_sum', 'annulus_sum_err', 'annulus_mean',
'annulus_mean_err', 'aperture_bkg', 'aperture_bkg_err']
for col in colnames:
tbl[col] = np.full(nimg, np.nan)
tbl['net_aperture_sum'] = aperture_sum
tbl['net_aperture_sum_err'] = aperture_sum_err
return tbl
import photometry cx, cy = (np.int_(np.mean(xcc)), np.int_(np.mean(ycc))) sx, sy = (np.int_(np.mean(xcs)), np.int_(np.mean(ycs))) radius = 5 r_in, r_out = 11, 14 # Companion: positions = (cx - 1, cy - 1) ap = CircularAperture(positions, r=radius) skyan = CircularAnnulus(positions, r_in=11, r_out=14) ap = CircularAperture(positions, r=radius) skyan = CircularAnnulus(positions, r_in=11, r_out=14) apsum = ap.do_photometry(image)[0] skysum = skyan.do_photometry(image)[0] averagesky = skysum / skyan.area() signal = (apsum - ap.area() * averagesky)[0] n = ap.area() box = image[cy + 12:cy + 12 + 15, cx + 12:cx + 12 + 15] noise = np.std(box) noise = noise * np.sqrt(n) compsnr = signal / noise # Star: positions = (sx - 1, sy - 1) ap = CircularAperture(positions, r=radius) skyan = CircularAnnulus(positions, r_in=11, r_out=14) ap = CircularAperture(positions, r=radius) skyan = CircularAnnulus(positions, r_in=11, r_out=14) apsum = ap.do_photometry(image)[0]
def smoothness(image: np.ndarray, mask: np.ndarray, centroid: List[float],
Rmax: float, r20: float, sky: float) -> float:
r'''Calculate the smoothness or clumpiness of the galaxy of interest.
.. math:: S = \frac{\sum \left|I - I_s\right| - B_s} {\sum \left|I\right|}
Where I is the image
:math:`I_s` is the smoothed image
:math:`B_s` is the background smoothness
see Lotz et al. 2004 https://doi.org/10.1086/421849
Parameters
----------
image : float, 2d np.ndarray
Image of galaxy
mask : float [0. - 1.], 2d np.ndarray
Mask which contains the pixels belonging to the galaxy of interest.
centroid : List[float]
Pixel location of the brightest pixel in galaxy.
Rmax : float
Distance from brightest pixel to furthest pixel in galaxy
r20 : float
Distance from brightest pixel to radius at which 20% of light of galaxy
is enclosed.
sky : float
Value of the sky background.
Returns
-------
Result: float
The smoothness or clumpiness parameter, S.
'''
r_in = r20
r_out = Rmax
# Exclude inner 20% of light. See Concelice 2003
imageApeture = CircularAnnulus(centroid, r_in, r_out)
# smooth image
imageSmooth = ndi.uniform_filter(image, size=int(r20))
# calculate residual, setting any negative pixels to 0.
imageDiff = image - imageSmooth
imageDiff[imageDiff < 0.] = 0.
# calculate S, accounting for the background smoothness.
imageFlux = imageApeture.do_photometry(image, method="exact")[0][0]
diffFlux = imageApeture.do_photometry(imageDiff, method="exact")[0][0]
backgroundSmooth = _getBackgroundSmoothness(image, mask, sky, r20)
S = (diffFlux - imageApeture.area * backgroundSmooth) / imageFlux
return S