def dered(
sne,
snname,
wave,
flux,
ivar,
source='not_swift_uv',
):
corrected = False
for j in range(len(sne)): # go through list of SN parameters
sn = sne[j][0]
if (snname.lower()
== sn.lower()[2:]) or (snname.lower() == sn.lower()) or (
snname.lower()[2:]
== sn.lower()): # SN with parameter matches the path
if not corrected:
# print 'Milky Way correction...'
if source != 'swift_uv' and source != 'foley_hst' and source != 'foundation':
b = sne[j][1].astype(float)
v = sne[j][2].astype(float)
bv = b - v
red = ex.reddening(wave,
a_v=3.1 * bv,
r_v=3.1,
model='f99')
flux *= red
ivar *= 1. / (red**2.)
corrected = True
else:
Av = sne[j][1].astype(float)
red = ex.reddening(wave, a_v=Av, r_v=3.1, model='f99')
flux *= red
ivar *= 1. / (red**2.)
corrected = True
return flux, ivar
def dered(sn_param,sne,filename,wave,flux):
for j in range(len(sn_param)):#go through list of SN parameters
sn = sn_param[j][0] #get relevent parameters needed for calculations
z = sn_param[j][1] # redshift value
if sn in filename:#SN with parameter matches the path
print "\n##############################################################\nlooking at",sne[j],"matched with",sn
b = sne[j][1].astype(float)
v = sne[j][2].astype(float)
bv = b-v
r = v/bv
print "B(%s)-V(%s)=%s"%(b,v,bv)
print "R(v) =",r
print "starting flux:\n",flux
#or use fm07 model
#test1 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='ccm89')
#test2 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='od94')
flux *= ex.reddening(wave,ebv = bv, r_v = 3.1, model='f99')
print "de-reddened with specutils f99 model:\n",flux
#print "de-reddened with specutils ccm89 model:\n",test1
#print "de-reddened with specutils od94 model:\n",test2
print "z:",z
print "starting wavelength:\n",wave
wave /= (1+z)
print "de-red-shifted wavelength:\n",wave
#print "de-reddened by host galaxy\n",flux*ex.reddening(wave,ebv = 0, r_v = r, model='f99')
#host *= ex.reddening(wave,ebv = bv, r_v = r, model='f99')
return [wave,flux]
def host_correction(spec, undo=False):
#TODO:finish, apply before scaling
wave = spec.wavelength[spec.x1:spec.x2]
flux = spec.flux[spec.x1:spec.x2]
ivar = spec.ivar[spec.x1:spec.x2]
if spec.av_25 != None:
Av_host = spec.av_25
rv = 2.5
elif spec.av_mlcs31 != None:
Av_host = spec.av_mlcs31
rv = 3.1
elif spec.av_mlcs17 != None:
Av_host = spec.av_mlcs17
rv = 1.7
else:
print 'No Host Correction'
return spec
wave_u = wave * u.Angstrom
flux_u = flux * u.Unit('W m-2 angstrom-1 sr-1')
spec1d = Spectrum1D.from_array(wave_u, flux_u)
spec1d_ivar = Spectrum1D.from_array(wave_u, ivar)
red = ex.reddening(spec1d.wavelength, a_v=Av_host, r_v=rv, model='f99')
if not undo:
flux_new = spec1d.flux * red
ivar_new = spec1d_ivar.flux * (1. / (red**2.))
else:
flux_new = spec1d.flux / red
ivar_new = spec1d_ivar.flux / (1. / (red**2.))
spec.flux[spec.x1:spec.x2] = flux_new
spec.ivar[spec.x1:spec.x2] = ivar_new
return spec
def correct_for_dust(wavelength, ra, dec):
"""Query IRSA dust map for E(B-V) value and returns reddening array
----------
wavelength : numpy array-like
Wavelength values for which to return reddening
ra : float
Right Ascencion in degrees
dec : float
Declination in degrees
Returns
-------
reddening : numpy array
Notes
-----
For info on the dust maps, see http://irsa.ipac.caltech.edu/applications/DUST/
"""
from astroquery.irsa_dust import IrsaDust
import astropy.coordinates as coord
import astropy.units as u
C = coord.SkyCoord(ra*u.deg, dec*u.deg, frame='fk5')
dust_image = IrsaDust.get_images(C, radius=2 *u.deg, image_type='ebv')[0]
ebv = np.mean(dust_image[0].data[40:42,40:42])
# print(ebv)
r_v = 3.1
av = r_v * ebv
from specutils.extinction import reddening
return reddening(wavelength* u.angstrom, av, r_v=r_v, model='ccm89'), ebv
def correct_for_dust(wavelength, ra, dec):
"""Query IRSA dust map for E(B-V) value and returns reddening array
----------
wavelength : numpy array-like
Wavelength values for which to return reddening
ra : float
Right Ascencion in degrees
dec : float
Declination in degrees
Returns
-------
reddening : numpy array
Notes
-----
For info on the dust maps, see http://irsa.ipac.caltech.edu/applications/DUST/
"""
from astroquery.irsa_dust import IrsaDust
import astropy.coordinates as coord
import astropy.units as u
C = coord.SkyCoord(ra*u.deg, dec*u.deg, frame='fk5')
dust_image = IrsaDust.get_images(C, radius=2 *u.deg, image_type='ebv', timeout=60)[0]
ebv = np.mean(dust_image[0].data[40:42, 40:42])
r_v = 3.1
av = r_v * ebv
from specutils.extinction import reddening
return reddening(wavelength* u.angstrom, av, r_v=r_v, model='ccm89'), ebv
def host_correction(sne, snname, wave, flux):
"""This function is deprecated. composite.py now uses
test_dered.host_correction() (yes that is a dumb file name)
"""
for j in range(len(sne)): # go through list of SN parameters
sn = sne[j][0]
if sn in snname: # SN with parameter matches the path
a_v = sne[j][2].astype(float)
flux *= ex.reddening(wave, ebv=3.1 * a_v, r_v=3.1, model='f99')
return flux
def deredden_fluxes(self):
"""Deredden the observed fluxes using the ccm89 model
The dereddening procedure is handled by the extinction.reddening method
from specutils.
"""
self.Av_gal = self.parameter_table.cols.Av_gal[0]
self.Av_host = self.parameter_table.cols.Av_host[0]
self.Av_tot = self.Av_gal + self.Av_host
for obs in self.converted_obs:
obs["flux"] = obs["flux"] * extinction.reddening(obs["wavelength"] * u.AA, self.Av_tot, model="ccm89")
def deredden_fluxes(self):
"""Deredden the observed fluxes using the ccm89 model
The dereddening procedure is handled by the extinction.reddening method
from specutils.
"""
self.Av_gal = self.parameter_table.cols.Av_gal[0]
self.Av_host = self.parameter_table.cols.Av_host[0]
self.Av_tot = self.Av_gal + self.Av_host
for obs in self.converted_obs:
obs['flux'] = obs['flux'] * extinction.reddening(
obs['wavelength'] * u.AA, self.Av_tot, model='ccm89')
def calculate_fbol(key, magnitudes, av):
wavelength_array, flux_array = build_flux_wl_array(key, magnitudes)
flux_array_unred = flux_array * extinction.reddening(wavelength_array, av, model='ccm89')
shortest_wl = np.amin(wavelength_array)
longest_wl = np.amax(wavelength_array)
fqbol = integrate_fqbol(wavelength_array, flux_array_unred)
temperature, angular_radius = bb_fit_parameters(wavelength_array,
flux_array_unred)
ir_corr = ir_correction(temperature.value, angular_radius, longest_wl.value)[0]
uv_corr = uv_correction_blackbody(temperature.value, angular_radius,
shortest_wl.value)[0]
fbol = fqbol.value + ir_corr + uv_corr
return fbol
def dered(z,sne,snname,wave,flux):
for j in range(len(sne)):#go through list of SN parameters
sn = sne[j][0]
if sn in snname:#SN with parameter matches the path
b = sne[j][1].astype(float)
v = sne[j][2].astype(float)
bv = b-v
r = v/bv
# print "B(%s)-V(%s)=%s"%(b,v,bv)
# print "R(v) =",r
#or use fm07 model
#test1 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='ccm89')
#test2 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='od94')
flux *= ex.reddening(wave,ebv = bv, r_v = 3.1, model='f99')
wave /= (1+z)
#print "de-reddened by host galaxy\n",flux*ex.reddening(wave,ebv = 0, r_v = r, model='f99')
#host *= ex.reddening(wave,ebv = bv, r_v = r, model='f99')
return [wave,flux]
def MW_correction(spec, undo=False):
#TODO:finish, apply before scaling
wave = spec.wavelength[spec.x1:spec.x2]
flux = spec.flux[spec.x1:spec.x2]
ivar = spec.ivar[spec.x1:spec.x2]
av_mw = spec.av_mw
wave_u = wave * u.Angstrom
flux_u = flux * u.Unit('W m-2 angstrom-1 sr-1')
spec1d = Spectrum1D.from_array(wave_u, flux_u)
spec1d_ivar = Spectrum1D.from_array(wave_u, ivar)
red = ex.reddening(spec1d.wavelength, a_v=av_mw, r_v=3.1, model='f99')
if not undo:
flux_new = spec1d.flux * red
ivar_new = spec1d_ivar.flux * (1. / (red**2.))
else:
flux_new = spec1d.flux / red
ivar_new = spec1d_ivar.flux / (1. / (red**2.))
spec.flux[spec.x1:spec.x2] = flux_new
spec.ivar[spec.x1:spec.x2] = ivar_new
return spec
def dered(sne, snname, wave, flux):
"""This function is deprecated. compprep() now uses
test_dered.dered() (yes that is a dumb file name)
"""
for j in range(len(sne)): # go through list of SN parameters
sn = sne[j][0]
if sn in snname: # SN with parameter matches the path
b = sne[j][1].astype(float)
v = sne[j][2].astype(float)
bv = b - v
# print "B(%s)-V(%s)=%s"%(b,v,bv)
# print "R(v) =",r
#or use fm07 model
#test1 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='ccm89')
#test2 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='od94')
flux *= ex.reddening(wave, ebv=bv, r_v=3.1, model='f99')
# wave /= (1+z)
#print "de-reddened by host galaxy\n",flux*ex.reddening(wave,ebv = 0, r_v = r, model='f99')
#host *= ex.reddening(wave,ebv = bv, r_v = r, model='f99')
return flux
def main():
#Generate data arrays
composite = np.genfromtxt('../data/Selsing2015.dat')
# composite = np.genfromtxt('../data/CompoM.dat')
wl, flux, error = composite[:, 0], composite[:, 1], composite[:, 1]
# dz = np.arange(1.2 , 2.7, 0.05)
dz = np.arange(0, 3, 0.01)
size_redshift = len(dz)
# bands = ['u', 'g', 'r', 'i', 'z', 'Z2', 'Y', 'J', 'H', 'K']
bands = ['g', 'r', 'J', 'K']
AV = np.array([0.0, 0.4, 0.8, 1.2, 1.6])
# AV = np.array([0.0, 0.5, 1.0])
# AV = np.array([0.0])
fig, ax = pl.subplots()
for c, av in enumerate(AV):
cmap = sns.cubehelix_palette(start=0.5 * c,
rot=0.0,
light=0.75,
dark=0.25,
as_cmap=True)
mags = collections.defaultdict(list)
#Loop through redshifts
for ii in dz:
#Redden at host
flux_dered = flux / reddening(
wl * u.angstrom, av, r_v=2.72, model='gcc09')
# error_dered = error / reddening(wl* u.angstrom, av, r_v=2.72, model='gcc09')
error_dered = 0
#Move with redshift
wl_z = wl * (1 + ii)
#Loop through bands
for k in bands:
# mag = synth_mag(band=k, datapath='../data/filter_curves/', wave=wl_z, flux=flux_dered, error=error_dered)
try:
mag = synth_mag_pysysp(wl_z,
flux_dered,
error_dered,
bandpath='../data/filter_curves/',
band=k)
except ValueError:
print('Filter outside composite range for band: ' +
str(k) + ' for redshift' + str(ii))
mags[k].append(np.nan)
continue
mags[k].append(mag)
#Calculate colors
JK = np.array(mags['J']) - np.array(mags['K'])
gJ = np.array(mags['g']) - np.array(mags['J'])
gr = np.array(mags['g']) - np.array(mags['r'])
#Printing
# print('J - K:', JK)
# print('J:', np.array(mags['J']))
# print('g - J:', gJ)
#Make the plot
ax.plot(JK,
gJ,
label=r'A$_{V}$ = ' + str(av),
lw=0.3,
zorder=1,
color=cmap(0.5),
alpha=1)
sca = ax.scatter(JK,
gJ,
c=dz,
zorder=2,
edgecolor='none',
alpha=1,
s=5,
cmap=cmap)
print(r'Plotted track for: A$_{V}$ = ' + str(av))
# cmap = sns.cubehelix_palette(start=1, rot=0.0, light=0.75, dark=0.25, as_cmap=True)
# sca = ax.scatter(JK, gJ, c=dz, zorder=2, edgecolor='none', alpha = 1, cmap=cmap)
ax.set_xlim((-1.0, 2.0))
ax.set_ylim((0.0, 4.0))
cbar = fig.colorbar(sca, ax=ax)
cbar.set_label('Redshift')
ax.set_xlabel('J - K')
ax.set_ylabel('g - J')
# cbar.set_label('z')
# set the linewidth of each legend object
leg = ax.legend(loc=2)
for legobj in leg.legendHandles:
legobj.set_linewidth(2.0)
pl.savefig('../figs/color_track_JKgJ.pdf')
pl.show()
def main():
#Generate data arrays
composite = np.genfromtxt('../data/Selsing2015.dat')
# composite = np.genfromtxt('../data/CompoM.dat')
wl, flux, error = composite[:,0], composite[:,1], composite[:,1]
# dz = np.arange(1.2 , 2.7, 0.05)
dz = np.arange(0 , 3, 0.01)
size_redshift = len(dz)
# bands = ['u', 'g', 'r', 'i', 'z', 'Z2', 'Y', 'J', 'H', 'K']
bands = ['g', 'r', 'J', 'K']
AV = np.array([0.0, 0.4, 0.8, 1.2, 1.6])
# AV = np.array([0.0, 0.5, 1.0])
# AV = np.array([0.0])
fig, ax = pl.subplots()
for c, av in enumerate(AV):
cmap = sns.cubehelix_palette(start=0.5 * c, rot=0.0, light=0.75, dark=0.25, as_cmap=True)
mags = collections.defaultdict(list)
#Loop through redshifts
for ii in dz:
#Redden at host
flux_dered = flux / reddening(wl* u.angstrom, av, r_v=2.72, model='gcc09')
# error_dered = error / reddening(wl* u.angstrom, av, r_v=2.72, model='gcc09')
error_dered= 0
#Move with redshift
wl_z = wl * (1+ii)
#Loop through bands
for k in bands:
# mag = synth_mag(band=k, datapath='../data/filter_curves/', wave=wl_z, flux=flux_dered, error=error_dered)
try:
mag = synth_mag_pysysp(wl_z, flux_dered, error_dered, bandpath='../data/filter_curves/', band=k)
except ValueError:
print('Filter outside composite range for band: '+str(k)+' for redshift' + str(ii))
mags[k].append(np.nan)
continue
mags[k].append(mag)
#Calculate colors
JK = np.array(mags['J']) - np.array(mags['K'])
gJ = np.array(mags['g']) - np.array(mags['J'])
gr = np.array(mags['g']) - np.array(mags['r'])
#Printing
# print('J - K:', JK)
# print('J:', np.array(mags['J']))
# print('g - J:', gJ)
#Make the plot
ax.plot(JK, gJ, label= r'A$_{V}$ = '+str(av), lw=0.3, zorder=1, color=cmap(0.5), alpha= 1)
sca = ax.scatter(JK, gJ, c=dz, zorder=2, edgecolor='none', alpha = 1, s=5, cmap=cmap)
print(r'Plotted track for: A$_{V}$ = '+str(av))
# cmap = sns.cubehelix_palette(start=1, rot=0.0, light=0.75, dark=0.25, as_cmap=True)
# sca = ax.scatter(JK, gJ, c=dz, zorder=2, edgecolor='none', alpha = 1, cmap=cmap)
ax.set_xlim((-1.0, 2.0))
ax.set_ylim((0.0, 4.0))
cbar = fig.colorbar(sca, ax=ax)
cbar.set_label('Redshift')
ax.set_xlabel('J - K')
ax.set_ylabel('g - J')
# cbar.set_label('z')
# set the linewidth of each legend object
leg = ax.legend(loc=2)
for legobj in leg.legendHandles:
legobj.set_linewidth(2.0)
pl.savefig('../figs/color_track_JKgJ.pdf')
pl.show()
#deredden to host galaxy for i in range(num):#go through selected spectra data for j in range(len(sn)):#go through list of SN parameters if sn[j] in file_path[i]:#SN with parameter matches the path print "\n##############################################################\nlooking at",sne[j],"matched with",sn[j] b = sne[j][1].astype(float) v = sne[j][2].astype(float) bv = b-v r = v/bv print "B(%s)-V(%s)=%s"%(b,v,bv) print "R(v) =",r print "starting flux:\n",spectra_data[i][:,1] #or use fm07 model #test1 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='ccm89') #test2 = spectra_data[i][:,1] * ex.reddening(spectra_data[i][:,0],ebv = bv, model='od94') spectra_data[i][:,1] *= ex.reddening(spectra_data[i][:,0],ebv = bv, r_v = 3.1, model='f99') print "de-reddened with specutils f99 model:\n",spectra_data[i][:,1] #print "de-reddened with specutils ccm89 model:\n",test1 #print "de-reddened with specutils od94 model:\n",test2 print "starting wavelength:\n",spectra_data[i][:,0] spectra_data[i][:,0] /= (1+z[j]) print "z:",z[j] print "de-red-shifted wavelength:\n",spectra_data[i][:,0] #print "de-reddened by host galaxy\n",spectra_data[i][:,1]*ex.reddening(spectra_data[i][:,0],ebv = 0, r_v = r, model='f99') #host *= ex.reddening(spectra_data[i][:,0],ebv = bv, r_v = r, model='f99') print "##############################################################\ndone de-reddening and de-redshifting" ############################################################################################################################################## ##############################################################################################################################################
def host_correction(a_v, r_v, snname, wave, flux, ivar, model='f99'):
# print 'Host correction...'
red = ex.reddening(wave, a_v=a_v, r_v=r_v, model=model)
flux *= red
ivar *= 1. / (red**2.) #correct ivar too
return flux, ivar
def dered(ebv, wave, flux):
r_v = 3.1
flux *= ex.reddening(wave, a_v=ebv * r_v, r_v=3.1, model='f99')
#need to return just the array!
return flux
