def duet_fluence_to_abmag(fluence, duet_no, duet=None, bandpass=None):
"""
Convert AB magnitude for a source into the number of source counts.
Parameters
----------
fluence: float
fluence in the bandpass that you're using in units (ph / cm2 / sec)
duet_no: int, 1 or 2
DUET channel
Other parameters
----------------
duet : `astroduet.config.Telescope` object
if None, allocate a new Telescope object
bandpass: array
DUET bandpass you're using
Returns
-------
AB magnitude in the band (ABmag)
Example
-------
>>> funit = u.ph / u.cm**2/u.s
>>> abmag = duet_fluence_to_abmag(0.01*funit, 1)
>>> np.isclose(abmag.value, 18.54584301)
True
"""
from astroduet.config import Telescope
if duet is None:
duet = Telescope()
band = getattr(duet, f'band{duet_no}')
spec = [1] * u.ph / (u.s * u.cm**2 * u.AA)
wave = [band['eff_wave'].to(u.AA).value] * u.AA
if bandpass is None:
bandpass = band['eff_width'].to(u.AA)
scale = (duet.apply_filters(wave, spec, duet_no)).value[0]
fluence_corr = fluence / scale
ABmag = (fluence_corr / bandpass).to(u.ABmag,
equivalencies=u.spectral_density(
band['eff_wave'].to(u.AA)))
return ABmag
def duet_abmag_to_fluence(ABmag, duet_no, duet=None, bandpass=None):
"""
Convert AB magnitude for a source into the number of source counts.
Parameters
----------
ABmag: float
AB magnitude in the bandpass that you're using
duet_no: int, 1 or 2
DUET channel
Other parameters
----------------
duet : `astroduet.config.Telescope` object
if None, allocate a new Telescope object
bandpass: array
DUET bandpass you're using
Returns
-------
Fluence in the band (ph / cm2 / sec)
Example
-------
>>> fluence = duet_abmag_to_fluence(20*u.ABmag, 1)
>>> np.isclose(fluence.value, 0.00262022)
True
"""
import numpy as np
from astroduet.config import Telescope
if duet is None:
duet = Telescope()
band = getattr(duet, f'band{duet_no}')
spec = [1] * u.ph / (u.s * u.cm**2 * u.AA)
wave = [band['eff_wave'].to(u.AA).value] * u.AA
if bandpass is None:
bandpass = band['eff_width'].to(u.AA)
scale = (duet.apply_filters(wave, spec, duet_no)).value[0]
funit = u.ph / u.cm**2 / u.s / u.AA # Spectral radiances per Hz or per angstrom
fluence = bandpass * ABmag.to(
funit, equivalencies=u.spectral_density(band['eff_wave'].to(u.AA)))
return fluence * scale
def panstarrs_to_duet(panmags, duet=None):
"""
Converts GALEX FUV and NUV ABmags into DUET 1 and DUET 2 ABmags, assuming flat Fnu
Parameters
----------
panmags: array
PanSTARRS AB magnitudes and errors, input as [[g, g_err, r, r_err, i, i_err, z, z_err, y, y_err],[]] without units
duet: Telescope instance
Returns
-------
duetfluences: Array with same shape as galmags, with panstarrs g, panstarrs r, DUET 1 and DUET 2 fluences.
badstars: number of stars that were not fitted because they had only two or less good magnitudes
badfits: number of stars where the fit failed due to a runtime error or value error after trying all initial guesses
Example
-------
>>> from astroduet.config import Telescope
>>> duet = Telescope()
>>> star = np.array([[11.,0.1,10.3,0.1,10,0.1,10,0.1,10,0.1]])
>>> duetfluences, badstars, badfits = panstarrs_to_duet(star,duet=duet)
>>> np.isclose(duetfluences['d1_fluence'][0],0.041547)
True
"""
from astropy.modeling.blackbody import FLAM
from scipy.optimize import curve_fit
from astroduet.bbmag import bbfunc, bb_abmag_fluence
from astropy.table import Table
if duet is None:
from astroduet.config import Telescope
duet = Telescope()
fluxunit = u.erg / u.s / u.cm**2
# Central wavelengths of PanSTARRS bands:
pswav = np.array([486.6, 621.5, 754.5, 867.9, 963.3]) * u.nm
duetfluences = Table(np.zeros(4),
names=('ps_g', 'ps_r', 'd1_fluence', 'd2_fluence'))
badstars = 0
badfits = 0
# Loop over stars:
for i, star in enumerate(panmags):
# Replace bad values with nan:
star[star == -999.] = np.nan
# Order and convert to magnitudes
mags = star[::2] * u.ABmag
magerrs = star[1::2]
# Find valid values:
valid = ~(np.isnan(mags))
# Convert to flux densities
fden = mags[valid].to(FLAM,
equivalencies=u.spectral_density(pswav[valid]))
snrs = 1. / (10.**(magerrs[valid] / 2.5) - 1.)
# Set snr to 10 for nan errors:
snrs[np.isnan(snrs)] = 10
fden_err = fden / snrs
# Filter for stars with only one good data point:
if len(fden) > 2:
# Fit blackbody:
try:
# Starting value for blackbody fit:
p0 = [5000, 1.E-8]
coeff, var_matrix = curve_fit(bbfunc,
pswav[valid].value,
fden.value,
p0=p0,
sigma=fden_err.value,
absolute_sigma=True)
except RuntimeError:
badfits += 1
continue
except ValueError:
try:
p0 = [10000, 1.E-8]
coeff, var_matrix = curve_fit(bbfunc,
pswav[valid].value,
fden.value,
p0=p0,
sigma=fden_err.value,
absolute_sigma=True)
except RuntimeError:
badfits += 1
continue
except ValueError:
try:
p0 = [5000, 1.E-9]
coeff, var_matrix = curve_fit(bbfunc,
pswav[valid].value,
fden.value,
p0=p0,
sigma=fden_err.value,
absolute_sigma=True)
except RuntimeError:
badfits += 1
continue
except ValueError:
try:
p0 = [10000, 1.E-9]
coeff, var_matrix = curve_fit(bbfunc,
pswav[valid].value,
fden.value,
p0=p0,
sigma=fden_err.value,
absolute_sigma=True)
except RuntimeError:
badfits += 1
continue
except ValueError:
try:
p0 = [5000, 1.E-10]
coeff, var_matrix = curve_fit(
bbfunc,
pswav[valid].value,
fden.value,
p0=p0,
sigma=fden_err.value,
absolute_sigma=True)
except RuntimeError:
badfits += 1
continue
except ValueError:
try:
p0 = [10000, 1.E-10]
coeff, var_matrix = curve_fit(
bbfunc,
pswav[valid].value,
fden.value,
p0=p0,
sigma=fden_err.value,
absolute_sigma=True)
except RuntimeError:
badfits += 1
continue
except ValueError:
badfits += 1
# Get DUET fluences:
duetfluence = bb_abmag_fluence(duet=duet,
bbtemp=coeff[0] * u.K,
bolflux=coeff[1] * fluxunit)
duetfluences.add_row(
[mags[0], mags[1], duetfluence[0], duetfluence[1]])
else:
badstars += 1
duetfluences.remove_row(0)
duetfluences['d1_fluence'].unit = u.ph / u.s / u.cm**2
duetfluences['d2_fluence'].unit = u.ph / u.s / u.cm**2
return duetfluences, badstars, badfits
def test_run_through_Telescope_methods():
duet = Telescope()
duet_offax = Telescope(config='reduced_baseline')
duet.info()
duet.update_bandpass()
duet.update_psf()
# duet.update_psf_vals()
duet.calc_radial_profile()
duet.calc_psf_fwhm()
duet.update_effarea()
duet.fluence_to_rate(1 * u.ph / u.s / u.cm**2)
duet.psf_model()
duet.compute_psf_norms()
def galex_to_duet(galmags, duet=None):
"""
Converts GALEX FUV and NUV ABmags into DUET 1 and DUET 2 ABmags, assuming flat Fnu
Parameters
----------
galmags: array
GALEX AB magnitudes, either as [[FUV1, ..., FUVN],[NUV1, ..., NUVN]] or as [[FUV1, NUV1],...,[FUVN, NUVN]]
Code assumes the first format if len(galmags) = 2
duet: Telescope instance
Returns
-------
duetmags: Array with same shape as galmags, with DUET 1 and DUET 2 ABmags.
Example
-------
>>> from astroduet.config import Telescope
>>> duet = Telescope()
>>> galmags = [20,20]
>>> duetmags = galex_to_duet(galmags, duet)
>>> np.allclose(duetmags, [20,20])
True
"""
from astropy.modeling.blackbody import FNU
if duet is None:
from astroduet.config import Telescope
duet = Telescope()
galex_fuv_lef = 151.6 * u.nm
galex_nuv_lef = 226.7 * u.nm
duet_1_lef = duet.band1['eff_wave']
duet_2_lef = duet.band2['eff_wave']
galex_fuv_nef = galex_fuv_lef.to(u.Hz, u.spectral())
galex_nuv_nef = galex_nuv_lef.to(u.Hz, u.spectral())
duet_1_nef = duet_1_lef.to(u.Hz, u.spectral())
duet_2_nef = duet_2_lef.to(u.Hz, u.spectral())
# Sort input array into FUV and NUV magnitudes
if len(galmags) == 2:
fuv_mag = galmags[0] * u.ABmag
nuv_mag = galmags[1] * u.ABmag
else:
fuv_mag = galmags[:, 0] * u.ABmag
nuv_mag = galmags[:, 1] * u.ABmag
# Convert GALEX magnitudes to flux densities
fuv_fnu = fuv_mag.to(FNU, u.spectral_density(galex_fuv_nef))
nuv_fnu = nuv_mag.to(FNU, u.spectral_density(galex_nuv_nef))
# Extrapolate to DUET bands assuming linear Fnu/nu
delta_fnu = (nuv_fnu - fuv_fnu) / (galex_nuv_nef - galex_fuv_nef)
d1_fnu = fuv_fnu + delta_fnu * (duet_1_nef - galex_fuv_nef)
d2_fnu = fuv_fnu + delta_fnu * (duet_2_nef - galex_fuv_nef)
# Convert back to magnitudes
d1_mag = d1_fnu.to(u.ABmag, u.spectral_density(duet_1_nef))
d2_mag = d2_fnu.to(u.ABmag, u.spectral_density(duet_2_nef))
# Construct output array
if len(galmags) == 2:
duetmags = np.array([d1_mag.value, d2_mag.value])
else:
duetmags = np.array([d1_mag.value, d2_mag.value]).transpose()
return duetmags
def convert_model(filename, name='NoName', duet=None):
'''
Reads in the EMGW shock breakout models, converts them to DUET fluences, and
writes out the resulting models to FITS files.
Parameters
----------
filename : string
Path to GRB shock file.
Other parameters
----------------
name : string
name to use for the model. Default is 'NoName'
'''
if duet is None:
duet = Telescope()
bandone = duet.bandpass1
bandtwo = duet.bandpass2
dist0 = 10*u.pc
shock_data = np.loadtxt(filename)
time = (shock_data[:,0]*u.d).to(u.s)
temps = shock_data[:,2]
bolflux = 10**shock_data[:,1]
# Set up outputs
shock_lc = Table([time,
np.zeros(len(time))*u.ABmag,
np.zeros(len(time))*u.ABmag,
np.zeros(len(time))*u.ph/(u.s*u.cm**2),
np.zeros(len(time))*u.ph/(u.s*u.cm**2)],
names=('time', 'mag_D1', 'mag_D2', 'fluence_D1', 'fluence_D2'),
meta={'name': name + ' at 10 pc',
'dist0_pc' : '{}'.format(dist0.to(u.pc).value)})
N = len(temps)
for k, t, bf in tqdm(list(zip(np.arange(N), temps, bolflux))):
t *= u.K
bf *= (u.erg/u.s) /(4 * np.pi * dist0**2)
band1_mag, band2_mag = bb_abmag(bbtemp=t, bolflux = bf,
bandone=bandone, bandtwo=bandtwo, val=True)
band1_fluence, band2_fluence = bb_abmag_fluence(bbtemp=t,
bolflux=bf)
shock_lc[k]['mag_D1'] = band1_mag
shock_lc[k]['mag_D2'] = band2_mag
shock_lc[k]['fluence_D1'] = band1_fluence.value
shock_lc[k]['fluence_D2'] = band2_fluence.value
shock_lc['mag_D1'].unit = None
shock_lc['mag_D2'].unit = None
return shock_lc
def bb_abmag_fluence(val=False, duet=None, **kwargs):
"""
Take a blackbody with a certain temperature and convert to photon rate in a band.
Other Parameters
----------------
val : boolean
Retrurns AB mags without units (False, default) or with Astropy units
duet: ``astroduet.conifg.Telescope() object``
If you've already instanced a duet telecope object, feed it in here.
Currently allows the use of the default bandpasses.
umag : float
Must have astropy AB units
Apparent U-band AB mag. Only used if other values not provided?
siwftmag : float
Must have astropy AB units. Apparent Swift magnitude (default is 22*u.ABmag)
ref : string
Band to use for reference magnitude; options are 'u', 'swift' ('swift')
bbtemp : float
Blackbody temperature to use (20000*ur.K)
dist : float
Distance of the source. swiftmags are assumed to be given at a reference
distance of 10 pc (I think?)
bolflux : float
Bolometric flux; if not 1, refmag and distance are ignored. Should have
units like (1*ur.erg/ur.cm**2/ur.s)
diag : boolean
SHow diagnostic inforamtion
Returns
-------
ABmag1, ABmag2
"""
import astropy.units as ur
import astropy.constants as cr
from astropy.modeling import models
from astropy.modeling.blackbody import FLAM
import numpy as np
from astroduet.config import Telescope
if duet is None:
duet = Telescope()
bbtemp = kwargs.pop('bbtemp', 20000. * ur.K)
umag = kwargs.pop('umag', 22 * ur.ABmag)
swiftmag = kwargs.pop('swiftmag', 22 * ur.ABmag)
dist = kwargs.pop('dist', 10 * ur.pc)
ref = kwargs.pop('ref', 'swift')
diag = kwargs.pop('diag', False)
dist0 = 10 * ur.pc
bolflux = kwargs.pop('bolflux', 1. * ur.erg / (ur.cm**2 * ur.s))
bandu = [340, 380] * ur.nm # For comparison purposes
bandsw = [
172.53, 233.57
] * ur.nm # Swift UVW2 effective band (lambda_eff +/- 0.5 width_eff)
wav = np.arange(1000, 9000) * ur.AA # Wavelength scale in 1 Angstrom steps
bb = models.BlackBody1D(
temperature=bbtemp,
bolometric_flux=bolflux) # Load the blackbody model
flux = bb(wav).to(FLAM, ur.spectral_density(wav))
# Get Swift reference AB mag
fluxden_sw = np.mean(flux[(wav >= bandsw[0].to(ur.AA))
& (wav <= bandsw[1].to(ur.AA))])
magsw = fluxden_sw.to(ur.ABmag,
equivalencies=ur.spectral_density(np.mean(bandsw)))
# Conver to flux AB mags across the band.
flux_ab = flux.to(ur.ABmag, equivalencies=ur.spectral_density(wav))
# Distance modulus
distmod = (5 * np.log10(dist / dist0)).value * ur.mag
# Set up input:
magoff = swiftmag - magsw
# Apply the distance modulus and the Swift reference offset
if (bolflux == 1. * ur.erg / (ur.cm**2 * ur.s)):
flux_mag = flux_ab + magoff + distmod
else:
flux_mag = flux_ab
# Convert back to flux
flux_conv = flux_mag.to(FLAM, equivalencies=ur.spectral_density(wav))
dw = 1 * ur.AA
ph_energy = (cr.h.cgs * cr.c.cgs / wav.cgs) / ur.ph
# Convert to photon flux.
ph_flux = flux_conv * dw / ph_energy
# Apply filters, QE, etc.
band1_fluence = duet.apply_filters(wav, ph_flux, diag=diag, **kwargs).sum()
band2_fluence = duet.apply_filters(wav,
ph_flux,
band=2,
diag=diag,
**kwargs).sum()
if diag:
print()
print('Compute ABmags in TD bands for blackbody')
print('Blackbody temperature: {}'.format(bbtemp))
print('Reference UVW2-band magnitude: {}'.format(swiftmag))
print('Distance: {} (Reference distance is 10 pc)'.format(dist))
print()
print('Flux density Swift: {}'.format(fluxden_sw))
print('Distance modulus: {}'.format(distmod))
print('Raw ABmag Swift: {}'.format(magsw))
print('Offset from Swift band: {}'.format(magoff))
print('Fluence band one: {}'.format(band1_fluence))
print('Fluence band two: {}'.format(band2_fluence))
print('')
if val:
return band1_fluence.value, band2_fluence.value
else:
return band1_fluence, band2_fluence
def sim_galaxy(patch_size,
pixel_size,
gal_type=None,
gal_params=None,
duet=None,
band=None,
duet_no=None):
'''
Return 2D array of a Sersic profile to simulate a galaxy
Required inputs:
patch_size = Axis sizes of returned galaxy patch in pixels (15,15)
pixel_size = Angular size of pixel (6 * ur.arcsec)
Optional inputs:
gal_type = String that loads a pre-built 'average' galaxy or allows custom definition
gal_params = Dictionary of parameters for Sersic model: ...
duet = Telescope instance
band = duet.bandpass (defaults to DUET1; deprecated)
duet_no = integer (1 or 2) for DUET bandpass
'''
from astropy.modeling.models import Sersic2D
from astroduet.utils import duet_abmag_to_fluence, duet_no_from_band
if duet is None:
duet = Telescope()
if band is None:
band = duet.bandpass1
if duet_no is None:
duet_no = duet_no_from_band(band)
x = np.linspace(-(patch_size[0] // 2), patch_size[0] // 2, patch_size[0])
y = np.linspace(-(patch_size[1] // 2), patch_size[1] // 2, patch_size[1])
x, y = np.meshgrid(x, y)
# Takes either a keyword or Sersic profile parameters
# Typical galaxy parameters based on Bai et al. (2013)
# Hardcoded for now, to-do: take distance as an input
if gal_type == 'spiral':
# A typical spiral galaxy at 100 Mpc
surface_mag = 26.2 * u.ABmag # surface brightness (per arcsec**2)
surface_rate = duet.fluence_to_rate(
duet_abmag_to_fluence(surface_mag, duet_no,
duet=duet)) # surface count rate at r_eff
amplitude = surface_rate * pixel_size.value**2 # surface brightness (per pixel)
r_eff = 16.5 / pixel_size.value
n = 1
theta = 0
ellip = 0.5
x_0, y_0 = r_eff, 0
elif gal_type == 'elliptical':
# A typical elliptical galaxy at 100 Mpc
surface_mag = 25.0 * u.ABmag
surface_rate = duet.fluence_to_rate(
duet_abmag_to_fluence(surface_mag, duet_no,
duet=duet)) # surface count rate at r_eff
amplitude = surface_rate * pixel_size.value**2 # surface brightness (per pixel)
r_eff = 12.5 / pixel_size.value
n = 4
theta = 0
ellip = 0.5
x_0, y_0 = r_eff, 0
elif gal_type == 'dwarf':
# A typical dwarf galaxy at 10 Mpc
surface_mag = 25.8 * u.ABmag
surface_rate = duet.fluence_to_rate(
duet_abmag_to_fluence(surface_mag, duet_no,
duet=duet)) # surface count rate at r_eff
amplitude = surface_rate * pixel_size.value**2 # surface brightness (per pixel)
r_eff = 70 / pixel_size
r_eff = r_eff.value
n = 4
theta = 0
ellip = 0.5
x_0, y_0 = r_eff, 0
elif (gal_type == 'custom') | (gal_type == None):
# Get args from gal_params, default to spiral values
surface_mag = gal_params.get('magnitude', 26) * u.ABmag
surface_rate = duet.fluence_to_rate(
duet_abmag_to_fluence(surface_mag, duet_no,
duet=duet)) # surface count rate at r_eff
amplitude = surface_rate * pixel_size.value**2 # surface brightness (per pixel)
r_eff = gal_params.get('r_eff', 16.5 / pixel_size.value)
n = gal_params.get('n', 1)
theta = gal_params.get('theta', 0)
ellip = gal_params.get('ellip', 0.5)
x_0 = gal_params.get('x_0', 16.5 / pixel_size.value)
y_0 = gal_params.get('y_0', 0)
mod = Sersic2D(amplitude=amplitude,
r_eff=r_eff,
n=n,
x_0=x_0,
y_0=y_0,
ellip=ellip,
theta=theta)
gal = mod(x, y)
return gal
def convert_sn_model(label, name='NoName', duet=None):
'''
Reads in the SNe models, converts them to DUET fluences, and
writes out the resulting models to FITS files.
Parameters
----------
filename : string
Path to SN shock file.
Other parameters
----------------
name : string
name to use for the model. Default is 'NoName'
'''
if duet is None:
duet = Telescope()
bandone = duet.bandpass1
bandtwo = duet.bandpass2
dist0 = 10*u.pc
temptable = \
Table.read(f'{label}_teff.txt', format='ascii', names=['time', 'T'])
radiustable = \
Table.read(f'{label}_radius.txt', format='ascii', names=['time', 'R'])
table = join(temptable, radiustable)
N = len(table['time'])
time = table['time'] * u.s
shock_lc = Table([time,
np.zeros(len(time))*u.ABmag,
np.zeros(len(time))*u.ABmag,
np.zeros(len(time))*u.ph/(u.s*u.cm**2),
np.zeros(len(time))*u.ph/(u.s*u.cm**2)],
names=('time', 'mag_D1', 'mag_D2', 'fluence_D1', 'fluence_D2'),
meta={'name': name + ' at 10 pc',
'dist0_pc' : '{}'.format(dist0.to(u.pc).value)})
bolflux = (table['T'] * u.K) ** 4 * const.sigma_sb.cgs * (
(table['R'] * u.cm) / dist0.to(u.cm)) ** 2
temps = table['T'] * u.K
for k, t, bf in tqdm(list(zip(np.arange(N), temps, bolflux))):
band1_mag, band2_mag = bb_abmag(bbtemp=t, bolflux = bf,
bandone=bandone, bandtwo=bandtwo, val=True)
band1_fluence, band2_fluence = bb_abmag_fluence(bbtemp=t,
bolflux=bf)
shock_lc[k]['mag_D1'] = band1_mag
shock_lc[k]['mag_D2'] = band2_mag
shock_lc[k]['fluence_D1'] = band1_fluence.value
shock_lc[k]['fluence_D2'] = band2_fluence.value
shock_lc['mag_D1'].unit = None
shock_lc['mag_D2'].unit = None
return shock_lc
def run_daophot(image,
threshold,
star_tbl,
niters=1,
snr_lim=5,
duet=None,
diag=False):
'''
Given an image and a PSF, go run DAOPhot PSF-fitting algorithm
'''
from photutils.psf import DAOPhotPSFPhotometry, IntegratedGaussianPRF
if duet is None:
duet = Telescope()
fwhm = (duet.psf_fwhm / duet.pixel).to('').value
# Fix star table columns
star_tbl['x_0'] = star_tbl['x']
star_tbl['y_0'] = star_tbl['y']
# Define a fittable PSF model
sigma = fwhm / (2. * np.sqrt(2 * np.log(2)))
# Simple Gaussian model to fit
#psf_model = IntegratedGaussianPRF(sigma=sigma)
#flux_norm = 1
# Use DUET-like PSF
#oversample = 2 # Needs to be oversampled but only minimally
#duet_psf_os = duet.psf_model(pixel_size=duet.pixel/oversample, x_size=12, y_size=12) # Even numbers work better
#psf_model = EPSFModel(duet_psf_os.array,oversampling=oversample)
#flux_norm = 1/oversample**2 # A quirk of constructing an oversampled ePSF using photutils
psf_model = duet.epsf_model
# Temporarily turn off Astropy warnings
import warnings
from astropy.utils.exceptions import AstropyWarning
warnings.simplefilter('ignore', category=AstropyWarning)
## FROM HERE ON NO UNITS ###########
# Initialise a Photometry object
# This object loops find, fit and subtract
threshold = threshold.to(image.unit)
photometry = DAOPhotPSFPhotometry(fwhm,
threshold.value,
fwhm,
psf_model, (5, 5),
niters=niters,
sigma_radius=5,
aperture_radius=fwhm)
# Problem with _recursive_lookup while fitting (needs latest version of astropy fix to modeling/utils.py)
result = photometry(image=image.value, init_guesses=star_tbl)
residual_image = photometry.get_residual_image()
# Filter results to only keep those with S/N greater than snr_lim (default is 5)
result_sig = result[np.abs(result['flux_fit'] /
result['flux_unc']) >= snr_lim]
if diag:
print("PSF-fitting complete")
# Turn warnings back on again
warnings.simplefilter('default')
## FROM HERE ON YES UNITS ###########
result_sig['flux_fit'] = result_sig['flux_fit'] * image.unit
result_sig['flux_unc'] = result_sig['flux_unc'] * image.unit
return result_sig, residual_image * image.unit
def construct_image(frame,
exposure,
duet=None,
band=None,
gal_type=None,
gal_params=None,
source=None,
source_loc=None,
sky_rate=None,
n_exp=1,
duet_no=None):
"""Construct a simualted image with an optional background galaxy and source.
1. Generate the empty image
2. Add galaxy (see sim_galaxy)
3. Add source (Poisson draw based on source*expossure)
4. Convolve with PSF
5. Rebin to the DUET pixel size.
6. Add in expected background rates per pixel and dark current.
7. Draw Poisson values and add read noise.
Parameters
----------
frame : ``numpy.array``
Number of pixel along x and y axis.
i.e., frame = np.array([30, 30])
exposure : ``astropy.units.Quantity``
Exposure time used for the light curve
Other parameters
----------------
duet : ``astroduet.config.Telescope``
If None, a default one is created
band : DUET bandpass (deprecated in favor of duet_no; defaults to DUET1)
gal_type : string
Default galaxy string ("spiral"/"elliptical") or "custom" w/ Sersic parameters
in gal_params
gal_params : dict
Dictionary of parameters for Sersic model (see sim_galaxy)
source : ``astropy.units.Quantity``
Source photon rate in ph / s; can be array for multiple sources
source_loc : ``numpy.array``
Coordinates of source(s) relative to frame (values between 0 and 1). If source is an array, source_loc must be the same length.
format: np.array([[X1,X2,X3,...,Xn],[Y1,Y2,Y3,...,Yn]])
sky_rate : ``astropy.units.Quantity``
Background photon rate in ph / s / pixel
n_exp : int
Number of simualted frames to co-add.
NB: I don't like this here!
duet_no : int (1 or 2)
DUET band number (defaults to DUET1)
Returns
-------
image : array with astropy.units
NxM image array with integer number of counts observed per pixel.
"""
from astroduet.utils import duet_no_from_band
assert type(
frame
) is np.ndarray, 'construct_image: Please enter frame as a numpy array'
# Load telescope parameters:
if duet is None:
duet = Telescope()
if band is None:
band = duet.bandpass1
if duet_no is None:
duet_no = duet_no_from_band(band)
read_noise = duet.read_noise
oversample = 6
pixel_size_init = duet.pixel / oversample
# Load the PSF kernel. Note that this does NOT HAVE POINTING JITTER!
psf_kernel = duet.psf_model(pixel_size=pixel_size_init)
# 1. Generate the empty image
# Initialise an image, oversampled by the oversample parameter to begin with
im_array = np.zeros(frame * oversample) * u.ph / u.s
# 2. Add a galaxy?
if gal_type is not None:
# Get a patch with a simulated galaxy on it
gal = sim_galaxy(frame * oversample,
pixel_size_init,
gal_type=gal_type,
gal_params=gal_params,
duet=duet,
duet_no=duet_no)
im_array += gal
# 3. Add a source?
if source is not None:
# Place source as a delta function at the center of the frame
if source_loc is None:
im_array[im_array.shape[0] // 2 + 1,
im_array.shape[1] // 2 + 1] += source
# Otherwise place sources at given source locations in frame
else:
source_inv = np.array([
source_loc[1], source_loc[0]
]) # Invert axes because python is weird that way
source_pix = (source_inv.transpose() *
np.array(im_array.shape)).transpose().astype(int)
im_array[tuple(source_pix)] += source
# Result should now be (floats) expected number of photons per pixel per second
# in the oversampled imae
# 4. Convolve with the PSF
im_psf = convolve_fft(im_array.value, psf_kernel) * im_array.unit
# Convolve again, now with the pointing jitter (need to re-apply units here as it's lost in convolution)
#im_psf = convolve(im_psf_temp, Gaussian2DKernel((duet.jitter_rms/pixel_size_init).value)) * im_array.unit
# 5. Bin up the image by oversample parameter to the correct pixel size
shape = (frame[0], oversample, frame[1], oversample)
im_binned = im_psf.reshape(shape).sum(-1).sum(1)
# 6. Add sky background (these are both given in ph / pix / s)
if sky_rate is not None:
# Add sky rate per pixel across the whole image
im_binned += sky_rate
# 6b: Add dark current:
im_binned += duet.dark_current
# Convert to expected counts -- TEMPORARY: .value transform photons in a number
im_counts = (im_binned * exposure)
# Co-add a number of separate exposures
im_final = np.zeros(frame)
for i in range(n_exp):
# Apply Poisson noise and instrument read noise. Note that read noise here
# is
im_noise = np.random.poisson(im_counts.value) + \
np.random.normal(loc=0, scale=read_noise,size=im_counts.shape)
im_noise = np.floor(im_noise)
im_noise[im_noise < 0] = 0
# Add to the co-add
im_final += im_noise
# Return image
return im_final * im_counts.unit
def filter_parameters(duet=None, *args, **kwargs):
"""
Construct the effective central wavelength and the effective bandpass
for the filters.
Parameters
----------
Other parameters
----------------
vega : conditional, default False
Use the Vega spetrum (9.8e3 K blackbody) to compute values. Otherwise computed
"flat" values if quoting AB mags.
diag : conditional, default False
Show the diagnostic info on the parameters.
Examples
--------
>>> band1, band2 = filter_parameters()
>>> allclose(band1['eff_wave'].value, 198.63858525)
True
"""
from astroduet.config import Telescope
if duet is None:
duet = Telescope()
from astropy.modeling import models
from astropy.modeling.blackbody import FNU, FLAM
from astropy import units as u
import numpy as np
vega = kwargs.pop('vega', False)
diag = kwargs.pop('diag', False)
wave = np.arange(1000, 10000) * u.AA
if vega:
temp = 9.8e3 * u.K
bb = models.BlackBody1D(temperature=temp)
flux = bb(wave).to(FLAM, u.spectral_density(wave))
else:
flat_model = np.zeros_like(wave.value)
flat_model += 1
flat_model *= FNU
flux = flat_model.to(FLAM, u.spectral_density(wave))
band1 = duet.apply_filters(wave, flux, band=1, **kwargs)
band2 = duet.apply_filters(wave, flux, band=2, **kwargs)
λ_eff1 = ((band1 * wave).sum() / (band1.sum())).to(u.nm)
λ_eff2 = ((band2 * wave).sum() / (band2.sum())).to(u.nm)
dλ = wave[1] - wave[0]
t1 = band1 / flux
t2 = band2 / flux
w1 = (dλ * t1.sum() / t1.max()).to(u.nm)
w2 = (dλ * t2.sum() / t2.max()).to(u.nm)
band1 = {'eff_wave': λ_eff1, 'eff_width': w1}
band2 = {'eff_wave': λ_eff2, 'eff_width': w2}
if diag:
print('Band1: {0:0.2f} λ_eff, {1:0.2f} W_eff'.format(λ_eff1, w1))
print('Band2: {0:0.2f} λ_eff, {1:0.2f} W_eff'.format(λ_eff2, w2))
return band1, band2
def imsim_srcdetect_combined(run='050719',
gal='spiral',
zodi='low',
nmags=71,
sfb=[20, 30],
stack=1):
"""
Run background estimation, image differencing and source detection on stacked simulated images
Assumes that the script is run in the directory that contains the run_... directory tree
Parameters
----------
run: string (date, as in '050719')
To track runs
zodi: 'low', 'med' or 'high', default is low
gal: 'spiral', 'elliptical', 'dwarf', or 'none'
sfb: [sfb_low, sfb_high], default is [20,30]
List of lowest and highest surface brightness that have been simulated
nmags: float, default is 71
Number of source magnitudes used in image simulations
stack: int, default is 1
Number of stacked exposures
Returns
-------
run_gal_zodi_band.fits: fits table with source detection results
"""
# Get telescope configuration from teldef file:
with open('run_' + run + '/teldef') as origin:
for line in origin:
if 'DUET Telescope State' in line:
tel = line.split(':')[1].strip('\n').strip()
# Initialize parameters
duet = Telescope(config=tel)
# Set up path
path1 = 'run_' + run + '/gal_' + gal + '/zodi_' + zodi + '/duet1/'
path2 = 'run_' + run + '/gal_' + gal + '/zodi_' + zodi + '/duet2/'
# Make galaxy surface brightness array
if gal != 'none':
sfb_arr = np.arange(sfb[0], sfb[1] + 1.).astype(str)
# Make source magnitude array
src_arr = np.linspace(20.5 - 0.5 * (nmags - 1) * 0.1,
20.5 + 0.5 * (nmags - 1) * 0.1,
num=nmags,
endpoint=True) # Currently in steps of 0.1 mag
# Set up results table
# columns: galaxy mag, source input mag, source input count rate, distance from galaxy center, reference depth, source detected True/False,
# if True: retrieved count rate, count rate error; number of false positives
tab = Table(np.zeros(9),
names=('galmag', 'srcmag', 'src-ctrate', 'dist', 'ref_depth',
'detected', 'ctrate', 'ctrate_err', 'false-pos'),
dtype=('f8', 'f8', 'f8', 'f8', 'i8', 'b', 'f8', 'f8', 'i8'),
meta={'name': gal + ' - ' + zodi + 'zodi - combined'})
print('Finding sources...')
if gal == 'none':
reffile1 = run + '_duet1_zodi-' + zodi + '_reference.fits'
hdu_ref1 = fits.open(path1 + reffile1)
reffile2 = run + '_duet2_zodi-' + zodi + '_reference.fits'
hdu_ref2 = fits.open(path2 + reffile2)
for srcmag in src_arr:
imfile1 = run + '_duet1_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
hdu_im1 = fits.open(path1 + imfile1)
imfile2 = run + '_duet2_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
hdu_im2 = fits.open(path2 + imfile2)
# Get input countrate
src_ctrate1 = duet.fluence_to_rate(
duet_abmag_to_fluence(srcmag * u.ABmag, 1, duet=duet))
src_ctrate2 = duet.fluence_to_rate(
duet_abmag_to_fluence(srcmag * u.ABmag, 2, duet=duet))
src_ctrate_comb = src_ctrate1 + src_ctrate2
# Run source detection for this set of HDUs:
tab = run_srcdetect_combined(hdu_ref1=hdu_ref1,
hdu_ref2=hdu_ref2,
hdu_im1=hdu_im1,
hdu_im2=hdu_im2,
tab=tab,
duet=duet,
sfb=np.nan,
srcmag=srcmag,
src_ctrate=src_ctrate_comb)
hdu_im1.close()
hdu_im2.close()
hdu_ref1.close()
hdu_ref2.close()
else:
for sfb in sfb_arr:
print('SFB: ' + sfb)
reffile1 = run + '_duet1_' + gal + '_' + sfb + '_zodi-' + zodi + '_reference.fits'
hdu_ref1 = fits.open(path1 + reffile1)
reffile2 = run + '_duet2_' + gal + '_' + sfb + '_zodi-' + zodi + '_reference.fits'
hdu_ref2 = fits.open(path2 + reffile2)
for srcmag in src_arr:
imfile1 = run + '_duet1_' + gal + '_' + sfb + '_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
hdu_im1 = fits.open(path1 + imfile1)
imfile2 = run + '_duet2_' + gal + '_' + sfb + '_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
hdu_im2 = fits.open(path2 + imfile2)
# Get input countrate
src_ctrate1 = duet.fluence_to_rate(
duet_abmag_to_fluence(srcmag * u.ABmag, 1, duet=duet))
src_ctrate2 = duet.fluence_to_rate(
duet_abmag_to_fluence(srcmag * u.ABmag, 2, duet=duet))
src_ctrate_comb = src_ctrate1 + src_ctrate2
# Run source detection for this set of HDUs:
tab = run_srcdetect_combined(hdu_ref1=hdu_ref1,
hdu_ref2=hdu_ref2,
hdu_im1=hdu_im1,
hdu_im2=hdu_im2,
tab=tab,
duet=duet,
sfb=float(sfb),
srcmag=srcmag,
src_ctrate=src_ctrate)
hdu_im1.close()
hdu_im2.close()
hdu_ref1.close()
hdu_ref2.close()
# Save output table
print('Writing file')
tab.remove_row(0)
tab.write('run' + run + '_gal-' + gal + '_zodi-' + zodi + '_stack-' +
str(stack) + '-combined.fits',
format='fits',
overwrite=True)
print('Done')
def imsim(**kwargs):
"""
Simulate images of sources in galaxies with a range of surface brightnesses
Warning! Takes several hours to run (~6 hours for 10 surface brightness levels, nmag=71 and nsrc=100)
Will make a directory tree run/galaxy/zodi-level/duet[1,2] in directory where it's run.
Parameters
----------
tel: 'config' default is 'baseline'
Sets telescope parameters
run: string (date, as in '050719', or other identifying string)
To track runs
gal: 'spiral', 'elliptical', 'dwarf' or 'none', default is spiral
Sets Sersic index and size
zodi: 'low', 'med' or 'high', default is low
Use the medium zodiacal background rate. Overrides low_zodi.
sfb: [sfb_low, sfb_high], default is [20,30]
List of lowest and highest surface brightness to simulate
nmags: int, default is 71
Number of source magnitudes to simulate, in 0.1 mag steps around 20.5
nsrc: int, default is 100
Number of sources to simulate at each source mag
stack: int, default is 1
Depth of science image (number of stacked 300s exposures)
nref: list, default is [1,3,7,11]
List of reference image depths
Returns
-------
telescope_band_gal_sfb_zodi_src-mag.fits: fits file with simulated images.
"""
# Deal with kwargs:
tel = kwargs.pop('tel', 'baseline')
gal = kwargs.pop('gal', 'spiral')
zodi = kwargs.pop('zodi', 'low')
sfb_lim = kwargs.pop('sfb', [20, 30])
nmags = kwargs.pop('nmags', 71)
nsrc = kwargs.pop('nsrc', 100)
run = kwargs.pop('run')
stack = kwargs.pop('stack', 1)
ref_arr = kwargs.pop('nref', [1, 3, 7, 11])
# set some telescope, instrument parameters
duet = Telescope(config=tel)
# Set/make directories:
path1 = sim_path(run=run, gal=gal, zodi=zodi, band='duet1')
path2 = sim_path(run=run, gal=gal, zodi=zodi, band='duet2')
# Write telescope definition file if it doesn't exist yet for this run:
if not os.path.exists('run_' + run + '/teldef'):
teldef = duet.info()
teldef_file = open('run_' + run + '/teldef', 'w+')
teldef_file.write(teldef)
teldef_file.close()
# Define image simulation parameters
exposure = 300 * u.s
frame = np.array(
[30, 30]
) # Dimensions of the image I'm simulating in DUET pixels (30x30 ~ 3x3 arcmin)
oversample = 6 # Hardcoded in construct_image
# Get backgrounds
if zodi == 'low':
[bgd_band1, bgd_band2] = background_pixel_rate(duet,
low_zodi=True,
diag=False)
elif zodi == 'med':
[bgd_band1, bgd_band2] = background_pixel_rate(duet,
med_zodi=True,
diag=False)
elif zodi == 'high':
[bgd_band1, bgd_band2] = background_pixel_rate(duet,
high_zodi=True,
diag=False)
# Define galaxy: magnitude is placeholder. Sizes are typical at 100 Mpc
if gal == 'spiral':
reff = 16.5 * u.arcsec
gal_params = {
'magnitude': 1,
'r_eff': reff / (duet.pixel / oversample),
'n': 1,
'x_0': 0,
'y_0': 0
}
elif gal == 'elliptical':
reff = 12.5 * u.arcsec
gal_params = {
'magnitude': 1,
'r_eff': reff / (duet.pixel / oversample),
'n': 4,
'x_0': 0,
'y_0': 0
}
elif gal == 'dwarf':
reff = 7 * u.arcsec
gal_params = {
'magnitude': 1,
'r_eff': reff / (duet.pixel / oversample),
'n': 1,
'x_0': 0,
'y_0': 0
}
elif gal == 'none':
gal_params = None
# Make galaxy surface brightness array (if necessary)
if gal != 'none':
sfb_arr = np.arange(sfb_lim[0],
sfb_lim[1] + 1.) # Now in steps of 1 mag
# Make srcmag array:
srcmag_arr = np.linspace(20.5 - 0.5 * (nmags - 1) * 0.1,
20.5 + 0.5 * (nmags - 1) * 0.1,
num=nmags,
endpoint=True) # Currently in steps of 0.1 mag
# No background galaxy:
if gal == 'none':
# Make reference images:
ref_hdu_1, ref_hdu_2 = run_sim_ref(duet=duet,
bkg1=bgd_band1,
bkg2=bgd_band2,
ref_arr=ref_arr,
gal=False,
exposure=exposure,
frame=frame)
# Update headers:
ref_hdu_1 = update_header(ref_hdu_1,
im_type='reference',
zodi=zodi,
gal=gal,
band='DUET1',
nframes=len(ref_arr),
exptime=exposure.value)
ref_hdu_2 = update_header(ref_hdu_2,
im_type='reference',
zodi=zodi,
gal=gal,
band='DUET2',
nframes=len(ref_arr),
exptime=exposure.value)
# Write files
ref_filename1 = run + '_duet1_zodi-' + zodi + '_reference.fits'
ref_hdu_1.writeto(path1 + '/' + ref_filename1, overwrite=True)
ref_filename2 = run + '_duet2_zodi-' + zodi + '_reference.fits'
ref_hdu_2.writeto(path2 + '/' + ref_filename2, overwrite=True)
# Make source images:
for srcmag in srcmag_arr:
src_hdu_1, src_hdu_2 = run_sim(duet=duet,
bkg1=bgd_band1,
bkg2=bgd_band2,
stack=stack,
srcmag=srcmag,
nsrc=nsrc,
gal=False,
exposure=exposure,
frame=frame)
# Update headers
src_hdu_1 = update_header(src_hdu_1,
im_type='source',
zodi=zodi,
gal=gal,
band='DUET1',
srcmag=srcmag,
nframes=nsrc,
exptime=exposure.value)
src_hdu_2 = update_header(src_hdu_2,
im_type='source',
zodi=zodi,
gal=gal,
band='DUET2',
srcmag=srcmag,
nframes=nsrc,
exptime=exposure.value)
# Write file
filename1 = run + '_duet1_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
src_hdu_1.writeto(path1 + '/' + filename1, overwrite=True)
filename2 = run + '_duet2_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
src_hdu_2.writeto(path2 + '/' + filename2, overwrite=True)
# Yes background galaxy:
else:
for i, sfb in enumerate(sfb_arr):
print('Surface brightness level ' + str(i + 1) + ' of ' +
str(len(sfb_arr)) + '...')
# Calculate count rate:
gal_params['magnitude'] = sfb
# Make reference images:
ref_hdu_1, ref_hdu_2 = run_sim_ref(duet=duet,
bkg1=bgd_band1,
bkg2=bgd_band2,
ref_arr=ref_arr,
gal=True,
gal_params=gal_params,
exposure=exposure,
frame=frame)
# Update headers:
ref_hdu_1 = update_header(ref_hdu_1,
im_type='reference',
zodi=zodi,
gal=gal,
band='DUET1',
nframes=len(ref_arr),
exptime=exposure.value)
ref_hdu_2 = update_header(ref_hdu_2,
im_type='reference',
zodi=zodi,
gal=gal,
band='DUET2',
nframes=len(ref_arr),
exptime=exposure.value)
# Write files:
ref_filename1 = run + '_duet1_' + gal + '_' + str(
sfb) + '_zodi-' + zodi + '_reference.fits'
ref_hdu_1.writeto(path1 + '/' + ref_filename1, overwrite=True)
ref_filename2 = run + '_duet2_' + gal + '_' + str(
sfb) + '_zodi-' + zodi + '_reference.fits'
ref_hdu_2.writeto(path2 + '/' + ref_filename2, overwrite=True)
# Make source images:
for srcmag in srcmag_arr:
src_hdu_1, src_hdu_2 = run_sim(duet=duet,
bkg1=bgd_band1,
bkg2=bgd_band2,
stack=stack,
srcmag=srcmag,
nsrc=nsrc,
gal=True,
gal_params=gal_params,
exposure=exposure,
frame=frame)
# Update headers:
src_hdu_1 = update_header(src_hdu_1,
im_type='source',
zodi=zodi,
gal=gal,
band='DUET1',
srcmag=srcmag,
nframes=nsrc,
exptime=exposure.value)
src_hdu_2 = update_header(src_hdu_2,
im_type='source',
zodi=zodi,
gal=gal,
band='DUET2',
srcmag=srcmag,
nframes=nsrc,
exptime=exposure.value)
# Write files:
filename1 = run + '_duet1_' + gal + '_' + str(
sfb) + '_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
src_hdu_1.writeto(path1 + '/' + filename1, overwrite=True)
filename2 = run + '_duet2_' + gal + '_' + str(
sfb) + '_zodi-' + zodi + '_stack-' + str(
stack) + '_src-' + "{:5.2f}".format(srcmag) + '.fits'
src_hdu_2.writeto(path2 + '/' + filename2, overwrite=True)