def wfc3_qso(outfil='Figures/wfc3_qso.pdf'):
""" Show a QSO that is transmissive at the Lyman limit
"""
# WFC3
wfc3, _ = pyicq.wfc3_continuum(0)
#zem = 4.
# Start the plot
xmnx = (650, 1300)
pp = PdfPages(outfil)
fig = plt.figure(figsize=(8.0, 5.0))
plt.clf()
gs = gridspec.GridSpec(1, 1)
# Lya line
ax = plt.subplot(gs[0])
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.xaxis.set_major_locator(plt.MultipleLocator(20.))
#ax.yaxis.set_minor_locator(plt.MultipleLocator(0.1))
#ax.yaxis.set_major_locator(plt.MultipleLocator(0.2))
ax.set_xlim(xmnx)
ax.set_ylim(0., 70)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Rest wavelength')
lw = 2.
# Data
ax.plot(wfc3.wavelength,
wfc3.flux,
'k',
linewidth=lw,
label='SDSS QSOs (z=4)')
# Label
csz = 17
ax.text(0.10,
0.80,
'HST/WFC3: QSO spectrum (z~2)',
color='black',
transform=ax.transAxes,
size=csz,
ha='left')
xputils.set_fontsize(ax, 17.)
# Layout and save
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2, h_pad=0.0, w_pad=0.4)
plt.subplots_adjust(hspace=0)
pp.savefig(bbox_inches='tight')
plt.close()
# Finish
pp.close()
def wfc3_qso(outfil='Figures/wfc3_qso.pdf'):
""" Show a QSO that is transmissive at the Lyman limit
"""
# WFC3
wfc3, _ = pyicq.wfc3_continuum(0)
#zem = 4.
# Start the plot
xmnx = (650, 1300)
pp = PdfPages(outfil)
fig = plt.figure(figsize=(8.0, 5.0))
plt.clf()
gs = gridspec.GridSpec(1,1)
# Lya line
ax = plt.subplot(gs[0])
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.xaxis.set_major_locator(plt.MultipleLocator(20.))
#ax.yaxis.set_minor_locator(plt.MultipleLocator(0.1))
#ax.yaxis.set_major_locator(plt.MultipleLocator(0.2))
ax.set_xlim(xmnx)
ax.set_ylim(0., 70)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Rest wavelength')
lw = 2.
# Data
ax.plot(wfc3.wavelength, wfc3.flux, 'k', linewidth=lw, label='SDSS QSOs (z=4)')
# Label
csz = 17
ax.text(0.10, 0.80, 'HST/WFC3: QSO spectrum (z~2)', color='black',
transform=ax.transAxes, size=csz, ha='left')
xputils.set_fontsize(ax, 17.)
# Layout and save
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2,h_pad=0.0,w_pad=0.4)
plt.subplots_adjust(hspace=0)
pp.savefig(bbox_inches='tight')
plt.close()
# Finish
pp.close()
def mk_mock(wave, zem, fN_model, out_spec=None, add_conti=True,
out_tbl=None, s2n=15., fwhm=3., seed=None):
""" Generate a mock
Parameters
----------
wave : Quantity array
zem : float
fN_model
out_spec : str, optional
out_tbl : str, optional
s2n : float, optional
fwhm : float, optional
seed : int, optional
Returns
-------
full_mock : XSpectrum1D of the mock
HI_comps : Table of the components
misc : tuple
Other bits and pieces [may deprecate]
"""
# Init
rstate=np.random.RandomState(seed)
# Wavelength Range
wvmin = np.min(wave) #(1+zem)*912.*u.AA - 1000*u.AA
wvmax = np.max(wave)
dwv = np.median(wave - np.roll(wave,1))
# zrange for Lya
zmin = (wvmin/(1215.6700*u.AA))-1.
# Components
HI_comps = monte_HIcomp((zmin,zem), fN_model, rstate=rstate)
# Main call
HIlines = mock_HIlines(HI_comps, (wvmin,wvmax))
# Optical depth
sub_wave, tot_tau = generate_tau(wave, HIlines, HI_comps)
dwv_sub = np.median(sub_wave-np.roll(sub_wave,1))
# Normalized mock spectrum (sub-grid of wavelengths)
sub_flux = np.exp(-1.*tot_tau)
sub_mock = XSpectrum1D.from_tuple( (sub_wave,sub_flux) )
# Smooth
smooth_mock = sub_mock.gauss_smooth(fwhm=fwhm*(dwv/dwv_sub))
# Rebin
mock = smooth_mock.rebin(wave)
# Add noise
mock.sig = np.ones(len(mock.flux))/s2n
noisy_mock = mock.add_noise(rstate=rstate)
# Continuum
if add_conti:
conti, wfc3_idx = pycq.wfc3_continuum(zqso=zem,wave=wave,rstate=rstate)
cflux = conti.flux
else:
cflux = np.ones_like(noisy_mock.flux)
wfc3_idx = -1
# Full
full_mock = XSpectrum1D.from_tuple((wave,noisy_mock.flux*cflux,
cflux*np.ones(len(noisy_mock.flux))/s2n))
# Write spectrum (as desired)
full_mock.meta.update(dict(zQSO=zem, S2N=s2n, seed=seed,
fN_gamma=fN_model.gamma, fN_type=fN_model.fN_mtype, conti=wfc3_idx))
if out_spec is not None:
full_mock.write_to_fits(out_spec, clobber=True)
# Save HI data (as desired)
if out_tbl is not None:
HI_comps.write(out_tbl, overwrite=True)
# Return
return full_mock, HI_comps, (sub_mock, tot_tau, mock)
def test_wfc3_conti():
wfc3, _ = pyicq.wfc3_continuum(wfc3_indx=0, zqso=2.)
np.testing.assert_allclose(wfc3.flux[100].value, 18.405926715695372)
def mk_mock(wave, zem, fN_model, out_spec=None, add_conti=True,
out_tbl=None, s2n=15., fwhm=3., seed=None):
""" Generate a mock
Parameters
----------
wave : Quantity array
zem : float
fN_model
out_spec : str, optional
out_tbl : str, optional
s2n : float, optional
fwhm : float, optional
seed : int, optional
Returns
-------
full_mock : XSpectrum1D of the mock
HI_comps : Table of the components
misc : tuple
Other bits and pieces [may deprecate]
"""
# Init
rstate=np.random.RandomState(seed)
# Wavelength Range
wvmin = np.min(wave) #(1+zem)*912.*u.AA - 1000*u.AA
wvmax = np.max(wave)
dwv = np.median(wave - np.roll(wave,1))
# zrange for Lya
zmin = (wvmin/(1215.6700*u.AA))-1.
# Components
HI_comps = monte_HIcomp((zmin,zem), fN_model, rstate=rstate)
# Main call
HIlines = mock_HIlines(HI_comps, (wvmin,wvmax))
# Optical depth
sub_wave, tot_tau = generate_tau(wave, HIlines, HI_comps)
dwv_sub = np.median(sub_wave-np.roll(sub_wave,1))
# Normalized mock spectrum (sub-grid of wavelengths)
sub_flux = np.exp(-1.*tot_tau)
sub_mock = XSpectrum1D.from_tuple( (sub_wave,sub_flux) )
# Smooth
smooth_mock = sub_mock.gauss_smooth(fwhm=fwhm*(dwv/dwv_sub))
# Rebin
mock = smooth_mock.rebin(wave)
# Add noise
mock.sig = np.ones(len(mock.flux))/s2n
noisy_mock = mock.add_noise(rstate=rstate)
# Continuum
if add_conti:
conti, wfc3_idx = pycq.wfc3_continuum(zqso=zem,wave=wave,rstate=rstate)
cflux = conti.flux
else:
cflux = np.ones_like(noisy_mock.flux)
wfc3_idx = -1
# Full
full_mock = XSpectrum1D.from_tuple((wave,noisy_mock.flux*cflux,
cflux*np.ones(len(noisy_mock.flux))/s2n))
# Write spectrum (as desired)
full_mock.meta.update(dict(zQSO=zem, S2N=s2n, seed=seed,
fN_gamma=fN_model.gamma, fN_type=fN_model.fN_mtype, conti=wfc3_idx))
if out_spec is not None:
full_mock.write_to_fits(out_spec, clobber=True)
# Save HI data (as desired)
if out_tbl is not None:
HI_comps.write(out_tbl, overwrite=True)
# Return
return full_mock, HI_comps, (sub_mock, tot_tau, mock)
def test_wfc3_conti():
wfc3, _ = pyicq.wfc3_continuum(wfc3_indx=0, zqso=2.)
np.testing.assert_allclose(wfc3.flux[100].value, 18.405926715695372)
