def test_telfer_and_igm():
telfer = pyicq.get_telfer_spec(zqso=3., igm=True, nproc=4)
# Test in forest
imin = np.argmin(np.abs(telfer.wavelength - 4800 * u.AA))
np.testing.assert_allclose(telfer.flux[imin].value,
1.7800761461257935,
atol=1e-3)
def init_conti_full(self):
print("Initializing the continuum")
spec = self.spec_widg.orig_spec
spec.select = self.model_spec # Just in case, but this should already be the case
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.wavelength, np.ones(len(spec.wavelength))))
self.conti_dict = pycc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=1215. * (1 + self.zqso),
#piv_wv2=915.*(1+zqso),
igm='True')
# Read Telfer and apply IGM
if self.template is not None:
tspec = lsi.readspec(self.template)
# assume wavelengths
tspec = XSpectrum1D.from_tuple(
(tspec.wavelength.value * (1 + self.zqso), tspec.flux.value))
else:
tspec = pycq.get_telfer_spec(
zqso=self.zqso, igm=(self.conti_dict['igm'] == 'True'))
# Rebin
self.continuum = tspec.rebin(spec.wavelength)
# Reset pivot wave
self.conti_dict['piv_wv'] = 915. * (1 + self.zqso)
#self.conti_dict['piv_wv'] = 1215.*(1+zqso)
#self.conti_dict['piv_wv2'] = 915.*(1+zqso)
self.base_continuum = self.continuum.flux
self.update_conti()
self.spec_widg.continuum = self.continuum
def qso_template(outfil='Figures/qso_template.pdf'):
""" van den berk
"""
pyigm_path = imp.find_module('pyigm')[1]
# Load
telfer = pyicq.get_telfer_spec()
clight = const.c.cgs
# Beta spliced to vanden Berk template with host galaxy removed
van_file = pyigm_path+'/data/quasar/VanDmeetBeta_fullResolution.txt'
van_tbl = Table.read(van_file,format='ascii')
isort = np.argsort(van_tbl['nu'])
nu_van = van_tbl['nu'][isort]
fnu_van = van_tbl['f_nu'][isort]
lam_van = (clight/(nu_van*u.Hz)).to('AA')
flam_van = fnu_van * clight / lam_van**2
nrm_pix = np.abs(lam_van-1450*u.AA) < 10*u.AA
nrm_van = np.median(flam_van[nrm_pix])
flam_van = flam_van / nrm_van
# Start the plot
xmnx = (1170., 2300)
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(ymnx)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Rest Wavelength (Angstroms)')
lw = 1.
ax.plot(telfer.wavelength, telfer.flux, 'k', linewidth=lw,
label='Telfer (z~1)')
ax.plot(lam_van, flam_van, 'b', linewidth=lw, label='SDSS (z~2)')
# Legend
legend = plt.legend(loc='upper right', scatterpoints=1, borderpad=0.3,
handletextpad=0.3, fontsize='large', numpoints=1)
# Layout and save
xputils.set_fontsize(ax, 17.)
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 qso_fuv(outfil='Figures/qso_fuv.pdf'):
""" FUV flux from QSOs
"""
pyigm_path = imp.find_module('pyigm')[1]
# Load
telfer = pyicq.get_telfer_spec()
# Start the plot
xmnx = (900., 1220)
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(ymnx)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Rest Wavelength (Angstroms)')
lw = 1.
ax.plot(telfer.wavelength,
telfer.flux,
'k',
linewidth=lw,
label='Telfer Average QSO SED (z~1)')
# Legend
legend = plt.legend(loc='upper left',
scatterpoints=1,
borderpad=0.3,
handletextpad=0.3,
fontsize='x-large',
numpoints=1)
# Layout and save
xputils.set_fontsize(ax, 17.)
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 qso_fuv(outfil='Figures/qso_fuv.pdf'):
""" FUV flux from QSOs
"""
pyigm_path = imp.find_module('pyigm')[1]
# Load
telfer = pyicq.get_telfer_spec()
# Start the plot
xmnx = (900., 1220)
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(ymnx)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Rest Wavelength (Angstroms)')
lw = 1.
ax.plot(telfer.wavelength, telfer.flux, 'k', linewidth=lw,
label='Telfer Average QSO SED (z~1)')
# Legend
legend = plt.legend(loc='upper left', scatterpoints=1, borderpad=0.3,
handletextpad=0.3, fontsize='x-large', numpoints=1)
# Layout and save
xputils.set_fontsize(ax, 17.)
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 __init__(self, ispec, parent=None, lls_fit_file=None,
outfil=None, smooth=3., zqso=None, fN_gamma=None, template=None,
dw=0.1, skip_wveval=False):
QtGui.QMainWindow.__init__(self, parent)
'''
ispec : Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
zqso : float, optional
Redshift of the quasar. If input, a Telfer continuum is used
fN_gamma : float, optional
Redshift evolution of f(N) or IGM fiddled continuum
template : str, optional
Filename of a QSO template to use instead of the Telfer
continuum. Only used if zqso is also given.
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.smooth = None
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
# this is broken
spec, spec_fil = ltgu.read_spec(ispec)
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(np.array([911.7, 949.743, 972.5367,1025.7222,1215.6700])*u.AA,
['LL','Lyd', 'Lyg','Lyb','Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
vlines = [(912 * (1 + zqso) if zqso is not None else None)]
self.spec_widg = ltgsp.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys,
vlines=vlines, plotzero=1)
# Initialize continuum (and LLS if from a file)
if lls_fit_file is not None:
self.init_LLS(lls_fit_file,spec)
else:
self.conti_dict = pycc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=1215.*(1+zqso),
#piv_wv2=915.*(1+zqso),
igm='True')
if self.base_continuum is None:
if zqso is not None:
self.zqso = zqso
# Read Telfer and apply IGM
if template is not None:
tspec = lsi.readspec(template)
# assume wavelengths
tspec = XSpectrum1D.from_tuple(
(tspec.dispersion.value * (1 + zqso),
tspec.flux.value))
else:
tspec = pycq.get_telfer_spec(zqso=zqso,
igm=(self.conti_dict['igm']=='True'))
# Rebin
self.continuum = tspec.rebin(spec.dispersion)
# Reset pivot wave
self.conti_dict['piv_wv'] = 915.*(1+zqso)
#self.conti_dict['piv_wv'] = 1215.*(1+zqso)
#self.conti_dict['piv_wv2'] = 915.*(1+zqso)
else:
self.zqso = None
self.continuum = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
self.base_continuum = self.continuum.flux
self.update_conti()
self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.dispersion,np.ones(len(spec.dispersion))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if lls_fit_file is not None:
self.update_boxes()
self.update_model()
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.zwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.bwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.Cwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
def obs_sawtooth(outfil='Figures/obs_sawtooth.pdf', all_tau=None, scl=1.):
""" Sawtooth opacity
"""
# SDSS
hdu = fits.open(
'/Users/xavier/paper/LLS/taueff/Analysis/stack_DR7_z3.92_z4.02.fits')
sdss_fx = hdu[0].data
sdss_wave = hdu[2].data
# Telfer
telfer = pyicq.get_telfer_spec()
i1450 = np.argmin(np.abs(telfer.wavelength.value - 1450.))
nrm = np.median(telfer.flux[i1450 - 5:i1450 + 5])
telfer.flux = telfer.flux / nrm
trebin = telfer.rebin(sdss_wave * u.AA)
# Load fN
fN_model = FNModel.default_model()
fN_model.zmnx = (2., 4.1) # extrapolate a bit
# teff
zem = 4.
wave = np.arange(4500., 6200., 10)
# Calculate
if all_tau is None:
all_tau = np.zeros_like(wave)
for qq, iwave in enumerate(wave):
all_tau[qq] = lyman_ew(iwave, zem, fN_model)
# Flux attenuation
trans = np.exp(-all_tau)
ftrans = interp1d(wave, trans, fill_value=1., bounds_error=False)
# Start the plot
xmnx = (4500, 6200)
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., 1.5)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Observed wavelength')
lw = 2.
# Data
ax.plot(sdss_wave * (1 + zem),
sdss_fx,
'k',
linewidth=lw,
label='SDSS QSOs (z=4)')
# Model
model = trebin.flux * ftrans(sdss_wave * (1 + zem)) * scl
ax.plot(sdss_wave * (1 + zem),
model,
'r',
linewidth=lw,
label='IGM+Telfer model')
# Label
csz = 17
#ax.text(0.10, 0.10, 'SDSS quasar stack at z=4', color='black',
# transform=ax.transAxes, size=csz, ha='left')
# Legend
legend = plt.legend(loc='upper left',
scatterpoints=1,
borderpad=0.3,
handletextpad=0.3,
fontsize='large',
numpoints=1)
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()
return all_tau
def redshift(outfil='Figures/redshift.pdf'):
""" Series of plots illustrating redshift in the Lya forest
"""
lrest = np.array([900., 1250]) # Ang
zem = 3.
toff = 0.15
yqso = 0.7
sqso = 35
# QSO lines
qsolya = AbsLine(1215.6700 * u.AA)
qsolya.attrib['N'] = 10.**(16.0) / u.cm**2
qsolya.attrib['b'] = 40 * u.km / u.s
qsolya.attrib['z'] = zem
qsolyb = AbsLine('HI 1025')
qsolyb.attrib['N'] = qsolya.attrib['N']
qsolyb.attrib['b'] = qsolya.attrib['b']
qsolyb.attrib['z'] = qsolya.attrib['z']
def tick_function(z, X):
V = X * (1 + z)
return ["{:d}".format(int(round(x))) for x in V]
def add_lines(axi, z):
wvtwo = (1 + z) * 1215.67 / (1 + zem)
axi.scatter([wvtwo], [yqso],
marker='o',
facecolor='none',
edgecolor='green',
s=sqso * 5)
axi.text(wvtwo,
yqso - 1.7 * toff,
'HI Gas (z={:0.1f})'.format(z),
color='green',
ha='center')
#
twolya = copy.deepcopy(qsolya)
twolya.attrib['z'] = z
twolyb = copy.deepcopy(qsolyb)
twolyb.attrib['z'] = z
return [twolya, twolyb]
# Telfer
telfer = pyicq.get_telfer_spec()
# Start the plot
pp = PdfPages(outfil)
scl = 1.0
fig = plt.figure(figsize=(8.0 * scl, 5.0 * scl))
plt.clf()
gs = gridspec.GridSpec(5, 1)
jet = cm = plt.get_cmap('jet')
# Loop
for qq in range(9):
# Cartoon
ax0 = plt.subplot(gs[0, 0])
ax0.set_xlim(lrest)
ax0.set_ylim(0., 1.)
ax0.set_frame_on(False)
ax0.axes.get_yaxis().set_visible(False)
ax0.axes.get_xaxis().set_visible(False)
# QSO
ax0.scatter([1215.67], [yqso], marker='o', facecolor='blue', s=sqso)
ax0.text(1215.67,
yqso + toff,
'Quasar (z=3)',
color='blue',
ha='center')
# Redshifted light
if qq > 0:
light = np.linspace(1215.67, lrest[0], 20)
ax0.scatter(light, [yqso] * len(light),
marker='_',
s=40,
cmap=cm,
c=1. / light)
# Gas at QSO
if qq > 1:
ax0.scatter([1215.67], [yqso],
marker='o',
facecolor='none',
edgecolor='green',
s=sqso * 5)
ax0.text(1215.67,
yqso - 1.7 * toff,
'HI Gas (z=3)',
color='green',
ha='center')
# Spectrum
ax = plt.subplot(gs[1:, 0])
ax.set_xlim(lrest)
#ax.set_ylim(ymnx)
ax.set_ylabel('Relative Flux')
ax.set_xlabel("Rest Wavelength")
if qq < 3:
tsty = 'k'
else:
tsty = 'b:'
ax.plot(telfer.wavelength, telfer.flux, tsty)
# Observer frame axis
if qq > 0:
ax2 = ax.twiny()
ax2.set_xlim(ax.get_xlim())
xtcks = ax.get_xticks()
ax2.set_xticks(xtcks)
ax2.set_xticklabels(tick_function(zem, xtcks))
ax2.set_xlabel('Observed Wavelength (Angstroms)')
# Absorption lines
abslines = []
if (qq > 2) and (qq != 8):
# Lya at zem
abslines.append(qsolya)
if qq > 3: # Lyb at zem
abslines.append(qsolyb)
# Gas at z=2.8
if qq > 4:
zadd = 2.8
abslines += add_lines(ax0, zadd)
# Gas at z=2.5
if qq > 5:
zadd = 2.5
abslines += add_lines(ax0, zadd)
if qq > 6:
zadd = 2.2
abslines += add_lines(ax0, zadd)
#
abs_model = ltav.voigt_from_abslines(telfer.wavelength * (1 + zem),
abslines)
#ax.plot(telfer.wavelength, telfer.flux*abs_model.flux, 'k')
ax.plot(telfer.wavelength, telfer.flux.value * abs_model.flux, 'k')
# Final plot
if qq == 8:
nlin = 100
dotwv = np.linspace(900, 1215., nlin)
ax0.scatter(dotwv, [yqso] * nlin,
marker='o',
facecolor='none',
edgecolor='green',
s=sqso * 5)
# Mock spectrum
fN_model = FNModel.default_model()
gdp = np.where(telfer.wavelength > 900. * u.AA)[0]
mock_spec, HI_comps, misc = pyimock.mk_mock(
telfer.wavelength[gdp] * (1 + zem),
zem,
fN_model,
s2n=100.,
fwhm=3,
add_conti=False)
ax.plot(telfer.wavelength[gdp],
telfer.flux[gdp].value * mock_spec.flux, 'k')
# Layout and save
plt.tight_layout(pad=0.2, h_pad=0.0, w_pad=0.4)
plt.subplots_adjust(hspace=0)
pp.savefig(bbox_inches='tight', transparent=True)
plt.close()
# Finish
print('Writing {:s}'.format(outfil))
pp.close()
return mock_spec
def qso_template(outfil='Figures/qso_template.pdf'):
""" van den berk
"""
pyigm_path = imp.find_module('pyigm')[1]
# Load
telfer = pyicq.get_telfer_spec()
clight = const.c.cgs
# Beta spliced to vanden Berk template with host galaxy removed
van_file = pyigm_path + '/data/quasar/VanDmeetBeta_fullResolution.txt'
van_tbl = Table.read(van_file, format='ascii')
isort = np.argsort(van_tbl['nu'])
nu_van = van_tbl['nu'][isort]
fnu_van = van_tbl['f_nu'][isort]
lam_van = (clight / (nu_van * u.Hz)).to('AA')
flam_van = fnu_van * clight / lam_van**2
nrm_pix = np.abs(lam_van - 1450 * u.AA) < 10 * u.AA
nrm_van = np.median(flam_van[nrm_pix])
flam_van = flam_van / nrm_van
# Start the plot
xmnx = (1170., 2300)
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(ymnx)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Rest Wavelength (Angstroms)')
lw = 1.
ax.plot(telfer.wavelength,
telfer.flux,
'k',
linewidth=lw,
label='Telfer (z~1)')
ax.plot(lam_van, flam_van, 'b', linewidth=lw, label='SDSS (z~2)')
# Legend
legend = plt.legend(loc='upper right',
scatterpoints=1,
borderpad=0.3,
handletextpad=0.3,
fontsize='large',
numpoints=1)
# Layout and save
xputils.set_fontsize(ax, 17.)
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 test_telfer_and_igm():
telfer = pyicq.get_telfer_spec(zqso=3., igm=True, nproc=4)
# Test
np.testing.assert_allclose(telfer.flux[100].value, 0.9383676133341446)
def test_telfer():
#
telfer = pyicq.get_telfer_spec(3.)
np.testing.assert_allclose(telfer.flux[100].value, 2.297435281318983)
def test_telfer():
#
telfer = pyicq.get_telfer_spec(3.)
np.testing.assert_allclose(telfer.flux[100].value, 2.297435281318983)
def __init__(self,
ispec,
parent=None,
lls_fit_file=None,
outfil=None,
smooth=3.,
zqso=None,
fN_gamma=None,
template=None,
dw=0.1,
skip_wveval=False,
norm=True):
QtGui.QMainWindow.__init__(self, parent)
'''
ispec : Spectrum1D or specfil
lls_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
zqso : float, optional
Redshift of the quasar. If input, a Telfer continuum is used
fN_gamma : float, optional
Redshift evolution of f(N) or IGM fiddled continuum
template : str, optional
Filename of a QSO template to use instead of the Telfer
continuum. Only used if zqso is also given.
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
'''
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'LLS_fit.json'
else:
self.outfil = outfil
self.count_lls = 0
self.lls_model = None
self.smooth = None
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
# this is broken
spec, spec_fil = ltgu.read_spec(ispec)
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(
np.array([911.7, 949.743, 972.5367, 1025.7222, 1215.6700]) * u.AA,
['LL', 'Lyd', 'Lyg', 'Lyb', 'Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_LLS=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(
[],
only_one=True,
no_buttons=True,
linelist=self.llist[self.llist['List']])
vlines = [(912 * (1 + zqso) if zqso is not None else None)]
self.spec_widg = ltgsp.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys,
vlines=vlines,
plotzero=1,
norm=norm)
# Initialize continuum (and LLS if from a file)
if lls_fit_file is not None:
self.init_LLS(lls_fit_file, spec)
else:
self.conti_dict = pycc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=1215. * (1 + zqso),
#piv_wv2=915.*(1+zqso),
igm='True')
if self.base_continuum is None:
if zqso is not None:
self.zqso = zqso
# Read Telfer and apply IGM
if template is not None:
tspec = lsi.readspec(template)
# assume wavelengths
tspec = XSpectrum1D.from_tuple(
(tspec.wavelength.value * (1 + zqso),
tspec.flux.value))
else:
tspec = pycq.get_telfer_spec(
zqso=zqso, igm=(self.conti_dict['igm'] == 'True'))
# Rebin
self.continuum = tspec.rebin(spec.wavelength)
# Reset pivot wave
self.conti_dict['piv_wv'] = 915. * (1 + zqso)
#self.conti_dict['piv_wv'] = 1215.*(1+zqso)
#self.conti_dict['piv_wv2'] = 915.*(1+zqso)
else:
self.zqso = None
self.continuum = XSpectrum1D.from_tuple(
(spec.wavelength, np.ones(len(spec.wavelength))))
self.base_continuum = self.continuum.flux
self.update_conti()
self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.wavelength, np.ones(len(spec.wavelength))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if lls_fit_file is not None:
self.update_boxes()
self.update_model()
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.zwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.bwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.Cwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
def obs_sawtooth(outfil='Figures/obs_sawtooth.pdf', all_tau=None, scl=1.):
""" Sawtooth opacity
"""
# SDSS
hdu = fits.open('/Users/xavier/paper/LLS/taueff/Analysis/stack_DR7_z3.92_z4.02.fits')
sdss_fx = hdu[0].data
sdss_wave = hdu[2].data
# Telfer
telfer = pyicq.get_telfer_spec()
i1450 = np.argmin(np.abs(telfer.wavelength.value - 1450.))
nrm = np.median(telfer.flux[i1450-5:i1450+5])
telfer.flux = telfer.flux / nrm
trebin = telfer.rebin(sdss_wave*u.AA)
# Load fN
fN_model = FNModel.default_model()
fN_model.zmnx = (2.,4.1) # extrapolate a bit
# teff
zem = 4.
wave = np.arange(4500., 6200., 10)
# Calculate
if all_tau is None:
all_tau = np.zeros_like(wave)
for qq,iwave in enumerate(wave):
all_tau[qq] = lyman_ew(iwave, zem, fN_model)
# Flux attenuation
trans = np.exp(-all_tau)
ftrans = interp1d(wave, trans, fill_value=1.,
bounds_error=False)
# Start the plot
xmnx = (4500, 6200)
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., 1.5)
ax.set_ylabel('Relative Flux')
ax.set_xlabel('Observed wavelength')
lw = 2.
# Data
ax.plot(sdss_wave*(1+zem), sdss_fx, 'k', linewidth=lw, label='SDSS QSOs (z=4)')
# Model
model = trebin.flux * ftrans(sdss_wave*(1+zem)) * scl
ax.plot(sdss_wave*(1+zem), model, 'r', linewidth=lw, label='IGM+Telfer model')
# Label
csz = 17
#ax.text(0.10, 0.10, 'SDSS quasar stack at z=4', color='black',
# transform=ax.transAxes, size=csz, ha='left')
# Legend
legend = plt.legend(loc='upper left', scatterpoints=1, borderpad=0.3,
handletextpad=0.3, fontsize='large', numpoints=1)
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()
return all_tau
def redshift(outfil='Figures/redshift.pdf'):
""" Series of plots illustrating redshift in the Lya forest
"""
lrest = np.array([900., 1250]) # Ang
zem = 3.
toff = 0.15
yqso = 0.7
sqso = 35
# QSO lines
qsolya = AbsLine(1215.6700*u.AA)
qsolya.attrib['N'] = 10.**(16.0)/u.cm**2
qsolya.attrib['b'] = 40 * u.km/u.s
qsolya.attrib['z'] = zem
qsolyb = AbsLine('HI 1025')
qsolyb.attrib['N'] = qsolya.attrib['N']
qsolyb.attrib['b'] = qsolya.attrib['b']
qsolyb.attrib['z'] = qsolya.attrib['z']
def tick_function(z, X):
V = X*(1+z)
return ["{:d}".format(int(round(x))) for x in V]
def add_lines(axi,z):
wvtwo = (1+z)*1215.67/(1+zem)
axi.scatter([wvtwo], [yqso], marker='o', facecolor='none',
edgecolor='green', s=sqso*5)
axi.text(wvtwo, yqso-1.7*toff, 'HI Gas (z={:0.1f})'.format(z),
color='green', ha='center')
#
twolya = copy.deepcopy(qsolya)
twolya.attrib['z'] = z
twolyb = copy.deepcopy(qsolyb)
twolyb.attrib['z'] = z
return [twolya, twolyb]
# Telfer
telfer = pyicq.get_telfer_spec()
# Start the plot
pp = PdfPages(outfil)
scl = 1.0
fig = plt.figure(figsize=(8.0*scl, 5.0*scl))
plt.clf()
gs = gridspec.GridSpec(5,1)
jet = cm = plt.get_cmap('jet')
# Loop
for qq in range(9):
# Cartoon
ax0 = plt.subplot(gs[0,0])
ax0.set_xlim(lrest)
ax0.set_ylim(0.,1.)
ax0.set_frame_on(False)
ax0.axes.get_yaxis().set_visible(False)
ax0.axes.get_xaxis().set_visible(False)
# QSO
ax0.scatter([1215.67], [yqso], marker='o', facecolor='blue', s=sqso)
ax0.text(1215.67, yqso+toff, 'Quasar (z=3)', color='blue', ha='center')
# Redshifted light
if qq > 0:
light = np.linspace(1215.67, lrest[0],20)
ax0.scatter(light, [yqso]*len(light), marker='_', s=40, cmap=cm, c=1./light)
# Gas at QSO
if qq > 1:
ax0.scatter([1215.67], [yqso], marker='o', facecolor='none',
edgecolor='green', s=sqso*5)
ax0.text(1215.67, yqso-1.7*toff, 'HI Gas (z=3)', color='green', ha='center')
# Spectrum
ax = plt.subplot(gs[1:,0])
ax.set_xlim(lrest)
#ax.set_ylim(ymnx)
ax.set_ylabel('Relative Flux')
ax.set_xlabel("Rest Wavelength")
if qq < 3:
tsty = 'k'
else:
tsty = 'b:'
ax.plot(telfer.wavelength, telfer.flux, tsty)
# Observer frame axis
if qq > 0:
ax2 = ax.twiny()
ax2.set_xlim(ax.get_xlim())
xtcks = ax.get_xticks()
ax2.set_xticks(xtcks)
ax2.set_xticklabels(tick_function(zem, xtcks))
ax2.set_xlabel('Observed Wavelength (Angstroms)')
# Absorption lines
abslines = []
if (qq > 2) and (qq != 8):
# Lya at zem
abslines.append(qsolya)
if qq > 3: # Lyb at zem
abslines.append(qsolyb)
# Gas at z=2.8
if qq > 4:
zadd = 2.8
abslines += add_lines(ax0, zadd)
# Gas at z=2.5
if qq > 5:
zadd = 2.5
abslines += add_lines(ax0, zadd)
if qq > 6:
zadd = 2.2
abslines += add_lines(ax0, zadd)
#
abs_model = ltav.voigt_from_abslines(telfer.wavelength*(1+zem), abslines)
#ax.plot(telfer.wavelength, telfer.flux*abs_model.flux, 'k')
ax.plot(telfer.wavelength, telfer.flux.value*abs_model.flux, 'k')
# Final plot
if qq == 8:
nlin = 100
dotwv = np.linspace(900,1215.,nlin)
ax0.scatter(dotwv, [yqso]*nlin, marker='o', facecolor='none',
edgecolor='green', s=sqso*5)
# Mock spectrum
fN_model = FNModel.default_model()
gdp = np.where(telfer.wavelength > 900.*u.AA)[0]
mock_spec, HI_comps, misc = pyimock.mk_mock(
telfer.wavelength[gdp]*(1+zem),
zem, fN_model, s2n=100., fwhm=3, add_conti=False)
ax.plot(telfer.wavelength[gdp],
telfer.flux[gdp].value*mock_spec.flux, 'k')
# Layout and save
plt.tight_layout(pad=0.2,h_pad=0.0,w_pad=0.4)
plt.subplots_adjust(hspace=0)
pp.savefig(bbox_inches='tight', transparent=True)
plt.close()
# Finish
print('Writing {:s}'.format(outfil))
pp.close()
return mock_spec
def test_telfer_and_igm():
telfer = pyicq.get_telfer_spec(zqso=3., igm=True, nproc=4)
# Test in forest
imin = np.argmin(np.abs(telfer.wavelength - 4800*u.AA))
np.testing.assert_allclose(telfer.flux[imin].value, 1.7800761461257935)