def redden(wave, flux, ebv_gal, ebv_host, z, R_gal=3.1, R_host=3.1,
redlaw='ccm', strict_ccm=False):
'''Artificially redden the spectral template to simulate dust reddening, a la
Cardelli et al.
Args:
wave (float array): Input wavelength in Angstroms
flux (float array): arbitrarily scaled SED flux
ebv_gal (float): color excess to be applied in rest-frame (due to MW)
ebv_host (floag): color excess to be applied at host redshift
z (float): redshift of the host extinction
R_gal (float): Ratio of total to selective absoption in V for restframe
component of extinction.
R_host (float): Ratio of total to selective absorption in V for host
frame extinction.
redlaw (str): Form of the dust extinction curve. Possible values are
'ccm', 'f99', or 'fm07'. See :mod:`snpy.utils.deredden`.
Returns:
float array: reddened flux.
'''
#First we redden due to galactic extinction:
newflux = 1.0*flux
# ebv_host is in the frame of the SN
if ebv_host != 0:
newflux,a,b = deredden.unred(wave, flux, -ebv_host, R_host,redlaw=redlaw,
strict_ccm=strict_ccm)
# ebv_gal is in the frame of the observer
if ebv_gal != 0:
newflux,a,b = deredden.unred(wave, newflux, -ebv_gal, R_gal, z,
redlaw=redlaw, strict_ccm=strict_ccm)
return(newflux)
def redden(wave,
flux,
ebv_gal,
ebv_host,
z,
R_gal=3.1,
R_host=3.1,
redlaw='ccm',
strict_ccm=False):
'''Artificially redden the spectral template to simulate dust reddening, a la
Cardelli et al.
Args:
wave (float array): Input wavelength in Angstroms
flux (float array): arbitrarily scaled SED flux
ebv_gal (float): color excess to be applied in rest-frame (due to MW)
ebv_host (floag): color excess to be applied at host redshift
z (float): redshift of the host extinction
R_gal (float): Ratio of total to selective absoption in V for restframe
component of extinction.
R_host (float): Ratio of total to selective absorption in V for host
frame extinction.
redlaw (str): Form of the dust extinction curve. Possible values are
'ccm', 'f99', or 'fm07'. See :mod:`snpy.utils.deredden`.
Returns:
float array: reddened flux.
'''
#First we redden due to galactic extinction:
newflux = 1.0 * flux
# ebv_host is in the frame of the SN
if ebv_host != 0:
newflux, a, b = deredden.unred(wave,
flux,
-ebv_host,
R_host,
redlaw=redlaw,
strict_ccm=strict_ccm)
# ebv_gal is in the frame of the observer
if ebv_gal != 0:
newflux, a, b = deredden.unred(wave,
newflux,
-ebv_gal,
R_gal,
z,
redlaw=redlaw,
strict_ccm=strict_ccm)
return (newflux)
def bolometric_SED(sn, bands=None, lam1=None, lam2=None, refband=None,
EBVhost=None, Rv=None, redlaw=None, extrap_red='RJ',
Tmax=None, interpolate=None, extrapolate=False, mopts={},
SED='H3', DM=None, cosmo='LambdaCDM', use_stretch=True,
extrap_SED=True, extra_output=False, verbose=False):
w,f = get_SED(0, version='H3')
if verbose: log("Starting bolometric calculation for %s\n" % sn.name)
if EBVhost is None:
EBVhost = getattr(sn, 'EBVhost', None)
if EBVhost is None:
raise AttributeError, "Error: you must either specify E(B-V) or "\
"fit a model that has EBVhost as a parameter"
if Rv is None:
Rv = getattr(sn, 'Rv', None)
if Rv is None:
raise AttributeError, "Error: you must either specify Rv or "\
"fit a model that has Rv as a parameter"
if redlaw is None:
redlaw = getattr(sn, 'redlaw', None)
if redlaw is None:
raise AttributeError, "Error: you must either specify redlaw or "\
"fit a model that has redlaw is defined"
if bands is None:
bands = getattr(sn.model, '_fbands', None)
if bands is None:
bands = sn.data.keys()
for b in bands:
if b not in sn.data:
raise AttributeError, "band %s not defined in data set" % (b)
# Bands must be increasing in wavelength
eff_waves = array([fset[b].eff_wave(w,f) for b in bands])
sids = argsort(eff_waves)
bands = [bands[i] for i in sids]
pars0 = {}
for b in bands: pars0[b] = 1.0
# Get itegration limits in SN restframe. So if we get it from the observer
# frame filter limits, we need to divide by (1+z)
if lam1 is None:
lam1 = array([fset[b].waverange()[0] for b in bands]).min()/(1+sn.z)
if lam2 is None:
lam2 = array([fset[b].waverange()[1] for b in bands]).max()/(1+sn.z)
if refband is not None:
if refband not in bands:
raise ValueError, "refband %s is not one of your observed filters" % \
refband
# We need a time of maximum to set the scale of the Hsiao templates
if Tmax is None:
Tmax = getattr(sn, 'Tmax', None)
if Tmax is None:
raise ValueError, "You must supply a time of B maximum or fit a "\
"model that has Tmax as a parameter"
# Now check that we can interpolate if needed
if interpolate is not None:
if interpolate == 'spline':
if verbose: log(" Using spline interpolation")
for b in bands:
if getattr(sn.data[b], 'interp', None) is None:
raise ValueError, "You asked for spline interpolation, but "\
"filter %s has not interpolator defined" % b
else:
if verbose: log(" Using model interpolation")
for b in bands:
if b not in sn.model._fbands:
raise ValueError, "You asked for model interpolation, but "\
"filter %f was not fit with the model" % b
else:
if verbose: log(" Not using interpolation")
if type(SED) is type(""):
# Assume it is a spectrum by name
if SED in ['H3','H','N','91bg']:
fSED = lambda x: get_SED(x, version=SED, extrapolate=True)
if verbose: log(" Using SED template '%s'" % SED)
elif SED in standards:
fSED = lambda x: (standards[SED].wave,standards[SED].flux)
if verbose: log(" Using standards['%s'] to compute effective wavelengths" % (SED))
else:
raise KeyError, "SED '%s' not found in standards database" % SED
elif type(SED) in [types.ListType,types.TupleType]:
if len(SED) != 2:
raise ValueError, "SED must be tuple or list of length 2"
fSED = lambda x: SED
elif type(SED) is types.FunctionType:
try:
w,f = SED(0)
except:
raise ValueError, "If SED is a function, it must take single" \
" argument (epoch) and return (wave,flux) tuple"
fSED = SED
else:
raise ValueError, "Unrecognized type (%s) for SED" % (type(SED))
s = 1.0
if use_stretch:
s = getattr(sn, 'st', None)
dm15 = getattr(sn, 'dm15', None)
if s is None:
if dm15 is None:
raise ValueError, "If you want to apply a stretch to the SED's, "\
"you must fit a model that uses dm15 or st as a parameter"
if dm15 > 1.7:
if verbose: log("Warning: dm15 > 1.7. Hsiao template is not "
"compatible with fast decliners. Proceed a your own risk")
s = kcorr.dm152s(1.7)
elif dm15 < 0.7:
if verbose: log("Warning: dm15 < 0.7. This is a very slow "
"decliner. Proceed at your own risk")
s = kcorr.dm152s(0.7)
else:
s = kcorr.dm152s(dm15)
if verbose: log(" Using a stretch of %f" % s)
# Now, we build up the times at which we will be integrating and the
# assocuated fluxes. We do things in the frame of the SN and de-stretch
# the times.
res = sn.get_mag_table(bands)
ts = (res['MJD'] - Tmax)/(1+sn.z)
# Restrict to valid interval of Eric's templates if extrap_SED is False
if not extrap_SED:
gids = greater_equal(ts/s, -19)*less_equal(ts/s,70)
else:
gids = -isnan(ts/s)
ts = ts[gids]
mags = []
masks = []
for b in bands:
mags.append(res[b][gids])
masks.append(less(res[b][gids],90))
if interpolate == 'spline':
# we fill in (where we can) missing data using splines
for i,b in enumerate(bands):
# interpolation is in the absolute time, so use MJD
mag,mask = sn.data[b].interp(res['MJD'][gids])
mags[i] = where(masks[i], mags[i], mag)
masks[i] = masks[i] + mask
elif interpolate == 'model':
# we fill in (where we can) missing data using the model
for i,b in enumerate(bands):
mag,emag,mask = sn.model(b, res['MJD'][gids], extrap=extrapolate)
mags[i] = where(masks[i], mags[i], mag)
masks[i] = masks[i] + mask
mags = transpose(array(mags))
masks = transpose(array(masks))
if verbose: log(" Working on data matrix with size (%d,%d)" % mags.shape)
# see if any days have zero data
gids = greater(sum(masks, axis=1), 0)
mags = mags[gids,:]
masks = masks[gids,:]
ts = ts[gids]
# Now mangle the spectra, deredden and integrate-em
filters_used = []
boloflux = []
epochs = []
mfuncs = []
fluxes = []
waves = []
parss = []
for i in range(len(ts)):
t = ts[i]
wave,flux = fSED(t/s)
# Check limits of integration (in rest frame of SN)
if lam1 < wave.min() or (lam2 > wave.max() and not extrap_red):
raise RuntimeError, "Error: your limits of integration (%.3f,%.3f) "\
"are outside the limits of the SED (%.3f,%.3f)" %\
(lam1,lam2,wave.min(), wave.max())
# integration limits
i1 = searchsorted(wave, lam1)
i2 = searchsorted(wave, lam2)
bs = [bands[j] for j in range(masks.shape[1]) if masks[i,j]]
if len(bs) == 1:
# No mangling possible
mflux = flux
mfuncs.append(flux*0+1)
else:
init = [pars0.get(b, 1.0) for b in bs]
mflux,ave_wave,pars = mangle_spectrum2(wave*(1+sn.z), flux, bs,
mags[i,masks[i]], normfilter=refband, init=init, **mopts)
mfuncs.append(mflux[0]/flux)
mflux = mflux[0]
for k,b in enumerate(bs):
pars0[b] = pars[k]
parss.append(pars)
# Now scale the spectrum to one of the observed filters
if refband is None:
idx = bands.index(bs[0])
filt = fset[bs[0]]
if verbose: log(" Using %s as reference filter" % bs[0])
else:
if refband not in bs:
if verbose: log("Warning: refband %s has no observation or "
"interpolation for epoch %f" % ts[i])
continue
idx = bands.index(refband)
filt = fset[refband]
# Scale to match photometry. We need to be careful here. The magnitude
# measures the response of the filter to the *redshifted* spectrum
mag = mags[i, idx]
mflux = mflux*power(10,
-0.4*(mag - filt.zp))/filt.response(wave, mflux/(1+sn.z), z=sn.z)
# Note: the quantity power()/filt.response() is actually
# dimensionless. Therefore mflux is in erg/s/cm^2/AA
# and *not* in photons
# Next, de-redden MW extinction and host extinction
mflux,a,b = deredden.unred(wave*(1+sn.z),mflux,sn.EBVgal,R_V=3.1,redlaw=redlaw)
mflux,a,b = deredden.unred(wave,mflux,EBVhost, R_V=Rv, redlaw=redlaw)
# Finally! integrate!
fbol = trapz(mflux[i1:i2], x=wave[i1:i2])
if lam2 > wave.max():
# add Rayleigh-Jeans extrapolation (~ 1/lam^4)
fbol += mflux[-1]*wave[-1]/3*(1 - power(wave[-1]/lam2,3))
filters_used.append(bs)
boloflux.append(fbol)
epochs.append(ts[i])
waves.append(wave[i1:i2])
fluxes.append(mflux[i1:i2])
boloflux = array(boloflux)
epochs = array(epochs)
# lastly, inverse-square law
if DM is None:
DM = sn.get_distmod(cosmo=cosmo)
dlum = power(10, 0.2*(DM+5))*3.086e18
boloflux = boloflux*4*pi*dlum**2
return(dict(epochs=array(epochs),
boloflux=array(boloflux),
filters_used=filters_used,waves=waves,fluxes=fluxes,
mfuncs=mfuncs, mags=mags, masks=masks, pars=parss))
def bolometric_SED(sn,
bands=None,
lam1=None,
lam2=None,
refband=None,
EBVhost=None,
Rv=None,
redlaw=None,
extrap_red='RJ',
Tmax=None,
interpolate=None,
extrapolate=False,
mopts={},
SED='H3',
DM=None,
cosmo='LambdaCDM',
use_stretch=True,
extrap_SED=True,
extra_output=False,
verbose=False):
w, f = get_SED(0, version='H3')
if verbose: log("Starting bolometric calculation for %s\n" % sn.name)
if EBVhost is None:
EBVhost = getattr(sn, 'EBVhost', None)
if EBVhost is None:
raise AttributeError, "Error: you must either specify E(B-V) or "\
"fit a model that has EBVhost as a parameter"
if Rv is None:
Rv = getattr(sn, 'Rv', None)
if Rv is None:
raise AttributeError, "Error: you must either specify Rv or "\
"fit a model that has Rv as a parameter"
if redlaw is None:
redlaw = getattr(sn, 'redlaw', None)
if redlaw is None:
raise AttributeError, "Error: you must either specify redlaw or "\
"fit a model that has redlaw is defined"
if bands is None:
bands = getattr(sn.model, '_fbands', None)
if bands is None:
bands = sn.data.keys()
for b in bands:
if b not in sn.data:
raise AttributeError, "band %s not defined in data set" % (b)
# Bands must be increasing in wavelength
eff_waves = array([fset[b].eff_wave(w, f) for b in bands])
sids = argsort(eff_waves)
bands = [bands[i] for i in sids]
pars0 = {}
for b in bands:
pars0[b] = 1.0
# Get itegration limits in SN restframe. So if we get it from the observer
# frame filter limits, we need to divide by (1+z)
if lam1 is None:
lam1 = array([fset[b].waverange()[0]
for b in bands]).min() / (1 + sn.z)
if lam2 is None:
lam2 = array([fset[b].waverange()[1]
for b in bands]).max() / (1 + sn.z)
if refband is not None:
if refband not in bands:
raise ValueError, "refband %s is not one of your observed filters" % \
refband
# We need a time of maximum to set the scale of the Hsiao templates
if Tmax is None:
Tmax = getattr(sn, 'Tmax', None)
if Tmax is None:
raise ValueError, "You must supply a time of B maximum or fit a "\
"model that has Tmax as a parameter"
# Now check that we can interpolate if needed
if interpolate is not None:
if interpolate == 'spline':
if verbose: log(" Using spline interpolation")
for b in bands:
if getattr(sn.data[b], 'interp', None) is None:
raise ValueError, "You asked for spline interpolation, but "\
"filter %s has not interpolator defined" % b
else:
if verbose: log(" Using model interpolation")
for b in bands:
if b not in sn.model._fbands:
raise ValueError, "You asked for model interpolation, but "\
"filter %f was not fit with the model" % b
else:
if verbose: log(" Not using interpolation")
if type(SED) is type(""):
# Assume it is a spectrum by name
if SED in ['H3', 'H', 'N', '91bg']:
fSED = lambda x: get_SED(x, version=SED, extrapolate=True)
if verbose: log(" Using SED template '%s'" % SED)
elif SED in standards:
fSED = lambda x: (standards[SED].wave, standards[SED].flux)
if verbose:
log(" Using standards['%s'] to compute effective wavelengths"
% (SED))
else:
raise KeyError, "SED '%s' not found in standards database" % SED
elif type(SED) in [types.ListType, types.TupleType]:
if len(SED) != 2:
raise ValueError, "SED must be tuple or list of length 2"
fSED = lambda x: SED
elif type(SED) is types.FunctionType:
try:
w, f = SED(0)
except:
raise ValueError, "If SED is a function, it must take single" \
" argument (epoch) and return (wave,flux) tuple"
fSED = SED
else:
raise ValueError, "Unrecognized type (%s) for SED" % (type(SED))
s = 1.0
if use_stretch:
s = getattr(sn, 'st', None)
dm15 = getattr(sn, 'dm15', None)
if s is None:
if dm15 is None:
raise ValueError, "If you want to apply a stretch to the SED's, "\
"you must fit a model that uses dm15 or st as a parameter"
if dm15 > 1.7:
if verbose:
log("Warning: dm15 > 1.7. Hsiao template is not "
"compatible with fast decliners. Proceed a your own risk"
)
s = kcorr.dm152s(1.7)
elif dm15 < 0.7:
if verbose:
log("Warning: dm15 < 0.7. This is a very slow "
"decliner. Proceed at your own risk")
s = kcorr.dm152s(0.7)
else:
s = kcorr.dm152s(dm15)
if verbose: log(" Using a stretch of %f" % s)
# Now, we build up the times at which we will be integrating and the
# assocuated fluxes. We do things in the frame of the SN and de-stretch
# the times.
res = sn.get_mag_table(bands)
ts = (res['MJD'] - Tmax) / (1 + sn.z)
# Restrict to valid interval of Eric's templates if extrap_SED is False
if not extrap_SED:
gids = greater_equal(ts / s, -19) * less_equal(ts / s, 70)
else:
gids = -isnan(ts / s)
ts = ts[gids]
mags = []
masks = []
for b in bands:
mags.append(res[b][gids])
masks.append(less(res[b][gids], 90))
if interpolate == 'spline':
# we fill in (where we can) missing data using splines
for i, b in enumerate(bands):
# interpolation is in the absolute time, so use MJD
mag, mask = sn.data[b].interp(res['MJD'][gids])
mags[i] = where(masks[i], mags[i], mag)
if extrapolate:
masks[i] = -isnan(mags[i])
else:
masks[i] = masks[i] + mask
elif interpolate == 'model':
# we fill in (where we can) missing data using the model
for i, b in enumerate(bands):
mag, emag, mask = sn.model(b, res['MJD'][gids], extrap=extrapolate)
mags[i] = where(masks[i], mags[i], mag)
masks[i] = masks[i] + mask
mags = transpose(array(mags))
masks = transpose(array(masks))
if verbose: log(" Working on data matrix with size (%d,%d)" % mags.shape)
# see if any days have zero data
gids = greater(sum(masks, axis=1), 0)
mags = mags[gids, :]
masks = masks[gids, :]
ts = ts[gids]
# Now mangle the spectra, deredden and integrate-em
filters_used = []
boloflux = []
epochs = []
mfuncs = []
fluxes = []
waves = []
parss = []
for i in range(len(ts)):
t = ts[i]
wave, flux = fSED(t / s)
# Check limits of integration (in rest frame of SN)
if lam1 < wave.min() or (lam2 > wave.max() and not extrap_red):
raise RuntimeError, "Error: your limits of integration (%.3f,%.3f) "\
"are outside the limits of the SED (%.3f,%.3f)" %\
(lam1,lam2,wave.min(), wave.max())
# integration limits
i1 = searchsorted(wave, lam1)
i2 = searchsorted(wave, lam2)
bs = [bands[j] for j in range(masks.shape[1]) if masks[i, j]]
if len(bs) == 1:
# No mangling possible
mflux = flux
mfuncs.append(flux * 0 + 1)
else:
init = [pars0.get(b, 1.0) for b in bs]
mflux, ave_wave, pars = mangle_spectrum2(wave * (1 + sn.z),
flux,
bs,
mags[i, masks[i]],
normfilter=refband,
init=init,
**mopts)
mfuncs.append(mflux[0] / flux)
mflux = mflux[0]
for k, b in enumerate(bs):
pars0[b] = pars[k]
parss.append(pars)
# Now scale the spectrum to one of the observed filters
if refband is None:
idx = bands.index(bs[0])
filt = fset[bs[0]]
if verbose: log(" Using %s as reference filter" % bs[0])
else:
if refband not in bs:
if verbose:
log("Warning: refband %s has no observation or "
"interpolation for epoch %f" % ts[i])
continue
idx = bands.index(refband)
filt = fset[refband]
# Scale to match photometry. We need to be careful here. The magnitude
# measures the response of the filter to the *redshifted* spectrum
mag = mags[i, idx]
mflux = mflux * power(10, -0.4 * (mag - filt.zp)) / filt.response(
wave, mflux / (1 + sn.z), z=sn.z)
# Note: the quantity power()/filt.response() is actually
# dimensionless. Therefore mflux is in erg/s/cm^2/AA
# and *not* in photons
# Next, de-redden MW extinction and host extinction
mflux, a, b = deredden.unred(wave * (1 + sn.z),
mflux,
sn.EBVgal,
R_V=3.1,
redlaw=redlaw)
mflux, a, b = deredden.unred(wave,
mflux,
EBVhost,
R_V=Rv,
redlaw=redlaw)
# Finally! integrate!
fbol = trapz(mflux[i1:i2], x=wave[i1:i2])
if lam2 > wave.max():
# add Rayleigh-Jeans extrapolation (~ 1/lam^4)
fbol += mflux[-1] * wave[-1] / 3 * (1 - power(wave[-1] / lam2, 3))
filters_used.append(bs)
boloflux.append(fbol)
epochs.append(ts[i])
waves.append(wave[i1:i2])
fluxes.append(mflux[i1:i2])
boloflux = array(boloflux)
epochs = array(epochs)
# lastly, inverse-square law
if DM is None:
DM = sn.get_distmod(cosmo=cosmo)
dlum = power(10, 0.2 * (DM + 5)) * 3.086e18
boloflux = boloflux * 4 * pi * dlum**2
return (dict(epochs=array(epochs),
boloflux=array(boloflux),
filters_used=filters_used,
waves=waves,
fluxes=fluxes,
mfuncs=mfuncs,
mags=mags,
masks=masks,
pars=parss))