def fig_qpq_sample(qpq7=None, outfil=None):
# Load QPQ7
if qpq7 is None:
qpq7 = equ.load_qpq(7)
bg_coord = SkyCoord(ra=qpq7['RAD_BG'], dec=qpq7['DECD_BG'], unit=u.deg)
fg_coord = SkyCoord(ra=qpq7['RAD'], dec=qpq7['DECD'], unit=u.deg)
# Small sep
gdsep = np.where(qpq7['R_PHYS'] < 300.)[0]
ngd = len(gdsep)
print('Nclose = {:d}'.format(ngd))
# Get PA, x, y
PA = []
for ii, gds in enumerate(gdsep):
PA.append(fg_coord[gds].position_angle(bg_coord[gds]))
PA = Quantity(PA)
x = qpq7['R_PHYS'][gdsep] * np.cos(PA)
y = qpq7['R_PHYS'][gdsep] * np.sin(PA)
if outfil is None:
outfil = 'fig_qpq_sample.pdf'
pp = PdfPages(outfil)
fig = plt.figure(figsize=(6.5, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
xpsimp.dark_bkgd(plt)
jet = cm = plt.get_cmap('jet')
ax = plt.subplot(gs[0, 0])
ax.set_frame_on(False)
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.xaxis.set_major_locator(plt.MultipleLocator(1.))
#ax.get_xaxis().get_major_formatter().set_useOffset(False)
ax.set_xlim(-300, 300)
ax.set_ylim(-300, 300)
#ax.set_xlabel('Relative Velocity (km/s)')
#ax.set_ylabel('Normalized Flux')
ax.get_xaxis().set_ticks([])
ax.get_yaxis().set_ticks([])
mplt = ax.scatter(x, y, c=qpq7['L_BOL'][gdsep], cmap=jet, edgecolor='none')
mplt.set_clim(vmin=45, vmax=47.)
cb = fig.colorbar(mplt)
cb.set_label(r'$\log \; L_{\rm Bol}$')
# Fonts
# Write
plt.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
print('Genereated {:s}'.format(outfil))
def fig_cos_dwarfs_images(outfil=None):
from xastropy.obs import x_getsdssimg as xgs
# Init COS-Dwarfs, COS-Halos
cos_dwarfs = COSDwarfs()
cos_dwarfs.load_mega(skip_ions=True)
cos_halos = COSHalos()
cos_halos.load_mega(skip_ions=True)
# Start the plot
if outfil is None:
outfil='fig_cos_dwarfs_images.pdf'
pp = PdfPages(outfil)
dx = 0.2
dy = 0.40
fig = plt.figure(figsize=(8, 5))
fig.clf()
# Setup for dark
xpsimp.dark_bkgd(plt)
gs = gridspec.GridSpec(1, 1)
# Axes
ax = plt.subplot(gs[0,0])
ax.set_xlim(8.0, 11.7)
#ax.xaxis.set_major_locator(plt.MultipleLocator(300.))
ax.set_ylim(-13,-8.2)
ax.set_ylabel('sSFR')
ax.set_xlabel('log M*')
iend = -1
#iend = 5
imsize = 0.3 # arcmin
for cgm_abs in cos_halos.cgm_abs[0:iend]:
img, oBW = xgs.getimg(cgm_abs.galaxy.coord.ra.deg,
cgm_abs.galaxy.coord.dec.deg, imsize=imsize)
# Figure out placement
ximg = cgm_abs.galaxy.stellar_mass
yimg = np.log10(cgm_abs.galaxy.sfr[1])-cgm_abs.galaxy.stellar_mass
# Show
scl=2.
ax.imshow(img,extent=(ximg-dx/scl, ximg+dx/scl, yimg-dy/scl, yimg+dy/scl),aspect=dx/dy)
iend = -1
#iend = 5
imsize = 0.8 # arcmin
for cgm_abs in cos_dwarfs.cgm_abs[0:iend]:
img, oBW = xgs.getimg(cgm_abs.galaxy.coord.ra.deg,
cgm_abs.galaxy.coord.dec.deg, imsize=imsize)
# Figure out placement
ximg = cgm_abs.galaxy.stellar_mass
yimg = np.log10(cgm_abs.galaxy.sfr[1])-cgm_abs.galaxy.stellar_mass
# Show
scl=2.
ax.imshow(img,extent=(ximg-dx/scl, ximg+dx/scl, yimg-dy/scl, yimg+dy/scl),aspect=dx/dy)
xputils.set_fontsize(ax,17.)
# Write
fig.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
plt.close()
# Finish
print('tlk_coshalos: Wrote {:s}'.format(outfil))
pp.close()
def fig_images(outfil=None):
from xastropy.obs import x_getsdssimg as xgs
# Init COS-Halos sightline
cos_halos = COSHalos()
cos_halos.load_mega(skip_ions=True)
#xdb.set_trace()
# Start the plot
if outfil is None:
outfil = 'fig_coshalo_images.pdf'
pp = PdfPages(outfil)
dx = 0.2
dy = 0.55
imsize = 1.2
for ss in range(5):
fig = plt.figure(figsize=(8, 5))
fig.clf()
# Setup for dark
xpsimp.dark_bkgd(plt)
gs = gridspec.GridSpec(1, 1)
# Axes
ax = plt.subplot(gs[0, 0])
ax.set_xlim(9.4, 11.7)
#ax.xaxis.set_major_locator(plt.MultipleLocator(300.))
ax.set_ylim(-13, -9)
ax.set_ylabel('sSFR')
ax.set_xlabel('log M*')
# Plot
if ss == 0:
mstar = [
cgm_abs.galaxy.stellar_mass for cgm_abs in cos_halos.cgm_abs
]
sSFR = [
np.log10(cgm_abs.galaxy.sfr[1]) - cgm_abs.galaxy.stellar_mass
for cgm_abs in cos_halos.cgm_abs
]
ax.scatter(mstar, sSFR)
elif ss == 1: # Show our first one
cgm_abs = cos_halos[('J0950+4831', '177_27')]
img, oBW = xgs.getimg(cgm_abs.galaxy.coord.ra.deg,
cgm_abs.galaxy.coord.dec.deg,
imsize=imsize)
# Figure out placement
ximg = cgm_abs.galaxy.stellar_mass
yimg = np.log10(
cgm_abs.galaxy.sfr[1]) - cgm_abs.galaxy.stellar_mass
# Show
ax.imshow(img,
extent=(ximg - dx, ximg + dx, yimg - dy, yimg + dy),
aspect=dx / dy)
elif ss == 2: # Show two
cgm_list = [('J0950+4831', '177_27'), ('J1245+3356', '236_36')]
for icgm in cgm_list:
cgm_abs = cos_halos[icgm]
img, oBW = xgs.getimg(cgm_abs.galaxy.coord.ra.deg,
cgm_abs.galaxy.coord.dec.deg,
imsize=imsize)
# Figure out placement
ximg = cgm_abs.galaxy.stellar_mass
yimg = np.log10(
cgm_abs.galaxy.sfr[1]) - cgm_abs.galaxy.stellar_mass
# Show
ax.imshow(img,
extent=(ximg - dx, ximg + dx, yimg - dy, yimg + dy),
aspect=dx / dy)
elif ss >= 3: # Show half
if ss == 3:
iend = 20
else:
iend = -1
for cgm_abs in cos_halos.cgm_abs[0:iend]:
img, oBW = xgs.getimg(cgm_abs.galaxy.coord.ra.deg,
cgm_abs.galaxy.coord.dec.deg,
imsize=1.2)
# Figure out placement
ximg = cgm_abs.galaxy.stellar_mass
yimg = np.log10(
cgm_abs.galaxy.sfr[1]) - cgm_abs.galaxy.stellar_mass
# Show
scl = 2.
ax.imshow(img,
extent=(ximg - dx / scl, ximg + dx / scl,
yimg - dy / scl, yimg + dy / scl),
aspect=dx / dy)
xputils.set_fontsize(ax, 17.)
# Write
fig.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
plt.close()
# Finish
print('tlk_coshalos: Wrote {:s}'.format(outfil))
pp.close()
def fig_kin_measures(outfil=None):
# Init COS-Halos sightline
cos_halos = COSHalos()
cos_halos.load_single( ('J1220+3853', '225_38') )
cgm_abs = cos_halos.cgm_abs[0]
#print('zem = {:g}'.format(cgm_abs.abs_sys.zem))
HI = 972.5368*u.AA
# ########################################
# Finder (out of order to avoid PDF issues)
#finder.main([cgm_abs.name, cgm_abs.galaxy.coord], imsize=2.*u.arcmin, show_circ=False)
# Start the plot
if outfil is None:
outfil='fig_kin_measures.pdf'
pp = PdfPages(outfil)
# dv
lclr = 'cyan'
vmnx = np.array([-350.,200.])*u.km/u.s
ymnx = (-0.05, 1.4)
for ss in range(2):
plt.figure(figsize=(5, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
xpsimp.dark_bkgd(plt)
# Axes
spec = cos_halos.load_bg_cos_spec(0, HI)
ax = plt.subplot(gs[0,0])
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.xaxis.set_major_locator(plt.MultipleLocator(1.))
#ax.get_xaxis().get_major_formatter().set_useOffset(False)
ax.set_xlim(vmnx.value)
ax.set_ylim(ymnx)
ax.set_xlabel('Relative Velocity (km/s)')
ax.set_ylabel('Normalized Flux')
# Zero line
ax.plot(vmnx.value, (0.,0.), ':', color='lightgreen')
ax.plot((0.,0.), ymnx, '--', color='lightgray')
# Data
velo = spec.relative_vel(HI*(cgm_abs.galaxy.z+1))
ax.plot(velo, spec.flux, color='white', drawstyle='steps')
# Label
if ss == 0:
ax.plot((-95,-95), ymnx, '--', color='cyan')
ax.text(-50., 1.2, r'$\delta v$', ha='center', fontsize=21., color=lclr)
elif ss == 1:
ax.plot((-170,-170), ymnx, '-', color='cyan')
ax.plot((60,60), ymnx, '-', color='cyan')
ax.text(-50., 1.2, r'$\Delta v$', ha='center', fontsize=21., color=lclr)
# Fonts
xputils.set_fontsize(ax,17.)
# Write
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
plt.close()
# ########################################
# Simple HI stack plot
trans = np.array([HI.value, 1031.9261])*u.AA
lbls = [r'HI Ly$\gamma$', 'OVI 1031']
plt.figure(figsize=(8, 5))
plt.clf()
gs = gridspec.GridSpec(2, 1)
for qq,itran,lbl in zip(range(len(trans)),trans,lbls):
# Load
spec = cos_halos.load_bg_cos_spec(0, itran)
# Axes
ax = plt.subplot(gs[qq,0])
ax.set_xlim(-500., 500.)
ax.set_ylim(-0.1, 1.3)
ax.set_ylabel('Normalized Flux')
if qq == 0:
ax.xaxis.set_ticklabels([])
else:
ax.set_xlabel('Relative Velocity (km/s)')
# Velo
velo = spec.relative_vel(itran*(cgm_abs.galaxy.z+1))
ax.plot(velo, spec.flux, color='white', drawstyle='steps', lw=1.3)
# Label
ax.text(-400., 0.2, lbl, ha='left', fontsize=21., color=lclr)
# Fonts
xputils.set_fontsize(ax,17.)
# Write
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
plt.close()
# Finish
print('tlk_coshalos: Wrote {:s}'.format(outfil))
pp.close()
def fig_cosdwarf_hist(outfil=None, cos_dwarfs=None):
# Init COS-Halos sightline
if cos_dwarfs is None:
cos_dwarfs = COSDwarfs()
cos_dwarfs.load_mega(skip_ions=True)
cos_dwarfs.load_abskin(flg=1)
# ########################################
# Finder (out of order to avoid PDF issues)
#finder.main([cgm_abs.name, cgm_abs.galaxy.coord], imsize=2.*u.arcmin, show_circ=False)
# Start the plot
if outfil is None:
outfil='fig_cosdwarf_kin_hist.pdf'
pp = PdfPages(outfil)
# dv
lclr = 'yellow'
plt.figure(figsize=(8, 4))
plt.clf()
xpsimp.dark_bkgd(plt)
gs = gridspec.GridSpec(1, 2)
for ss in range(2):
ax = plt.subplot(gs[ss])
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.get_xaxis().get_major_formatter().set_useOffset(False)
if ss == 0:
xmnx = [-400., 400.] # km/s
ymnx = (0, 10)
ax.set_xlabel(r'$\delta v$ (km/s)')
binsz = 25.
gdk = cos_dwarfs.abs_kin('HI')['flg'] > 0
val = cos_dwarfs.abs_kin('HI')['delta_v'][gdk]
ax.text(-200., 8, 'HI', ha='left', fontsize=21., color=lclr)
ax.xaxis.set_major_locator(plt.MultipleLocator(200.))
elif ss == 1:
xmnx = [0., 400.] # km/s
ymnx = (0, 10)
ax.set_xlabel(r'$\Delta v$ (km/s)')
val = cos_dwarfs.abs_kin('HI')['Dv'][gdk]
ax.xaxis.set_major_locator(plt.MultipleLocator(100.))
ax.set_ylabel('N')
ax.set_xlim(xmnx)
ax.set_ylim(ymnx)
ax.minorticks_on()
# Zero line
#ax.plot(vmnx.value, (0.,0.), ':', color='lightgreen')
#ax.plot((0.,0.), ymnx, '--', color='lightgray')
# Histogram
bins = np.arange(xmnx[0], xmnx[1] + binsz, binsz)
ax.hist(val, bins=bins, color='yellow', histtype='stepfilled',
edgecolor='white')
# Labels
#ax.text(-50., 1.2, r'$\Delta v$', ha='center', fontsize=21., color=lclr)
# Fonts
xputils.set_fontsize(ax,17.)
# Write
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
plt.close()
# Finish
print('tlk_cgm_kin: Wrote {:s}'.format(outfil))
pp.close()
def fig_coshalo_corr(outfil=None, cos_halos=None):
# Init COS-Halos sightline
if cos_halos is None:
cos_halos = COSHalos()
cos_halos.load_mega(skip_ions=True)
cos_halos.load_abskin(flg=1)
# ########################################
# Finder (out of order to avoid PDF issues)
#finder.main([cgm_abs.name, cgm_abs.galaxy.coord], imsize=2.*u.arcmin, show_circ=False)
# Start the plot
if outfil is None:
outfil='fig_coshalo_kin_corr.pdf'
pp = PdfPages(outfil)
# dv
lclr = 'cyan'
plt.figure(figsize=(8, 4))
plt.clf()
xpsimp.dark_bkgd(plt)
gs = gridspec.GridSpec(2, 3)
dv_ymnx = [-300., 290.] # km/s
Dv_ymnx = [0., 410.] # km/s
gdk = cos_halos.abs_kin('Metal')['flg'] > 0
for ss in range(6):
ax = plt.subplot(gs[ss%2,ss/2])
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.get_xaxis().get_major_formatter().set_useOffset(False)
if (ss/2) == 0: # dv vs. rho
xmnx = (0, 150.)
xlbl = r'$\rho$ (kpc)'
xval = cos_halos.rho.value[gdk]
elif (ss/2) == 1:
xmnx = (9, 12.)
xlbl = r'$\log M*$'
xval = cos_halos.stellar_mass[gdk]
elif (ss/2) == 2:
xmnx = (-13., -8)
xlbl = 'sSFR'
sfr = [float(sfr[1]) for sfr in cos_halos.sfr]
xval = (np.log10(sfr)-cos_halos.stellar_mass)[gdk]
#
ax.set_xlim(xmnx)
if ss == 0:
ax.set_ylabel(r'$\delta v$ (km/s)')
elif ss == 1:
ax.set_ylabel(r'$\Delta v$ (km/s)')
if (ss%2) == 0:
ax.xaxis.set_ticklabels([])
ymnx = dv_ymnx
yval = cos_halos.abs_kin('Metal')['delta_v'][gdk]
else:
ymnx = Dv_ymnx
yval = cos_halos.abs_kin('Metal')['Dv'][gdk]
ax.set_xlabel(xlbl)
ax.set_ylim(ymnx)
ax.minorticks_on()
#ax.xaxis.set_major_locator(plt.MultipleLocator(100.))
# Zero line
#ax.plot(vmnx.value, (0.,0.), ':', color='lightgreen')
#ax.plot((0.,0.), ymnx, '--', color='lightgray')
# Scatter plot
ax.scatter(xval, yval, marker='o', color='cyan')
# Labels
#ax.text(-50., 1.2, r'$\Delta v$', ha='center', fontsize=21., color=lclr)
# Fonts
xputils.set_fontsize(ax,13.)
# Write
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
plt.close()
# Finish
print('tlk_coshalos: Wrote {:s}'.format(outfil))
pp.close()
def fig_cii_star(qpq7=None, outfil=None):
""" Simple CII* plot for two systemsj
"""
# Spec files
# Load QPQ7
#if qpq7 is None:
# qpq7 = equ.load_qpq(7)
if outfil is None:
outfil = 'fig_qpq_ciistar.pdf'
pp = PdfPages(outfil)
fig = plt.figure(figsize=(6.5, 5))
plt.clf()
gs = gridspec.GridSpec(2, 2)
xpsimp.dark_bkgd(plt)
qpq8_sys = ['J142758.73-012136.1', 'J120416.68+022110.9']
#qpq8_sys = ['J120416.68+022110.9']
qpq8_zfg = [2.2736, 2.4358]
qpq8_vmnx = [(700, 880), (600, 770)]
trans = [1334.5323, 1335.7077]
lbls = ['CII 1334', 'CII* 1335']
for qq, qsys in enumerate(qpq8_sys):
# Load spectrum
sdict = eqs.spec_wvobs(qsys,
trans[0] * (1 + qpq8_zfg[qq]) * u.AA,
high_res=2)
spec = sdict['spec']
spec.normalize(sdict['conti'])
# Loop on transitions
for jj, itrans in enumerate(trans):
ax = plt.subplot(gs[jj, qq])
ax.set_xlim(qpq8_vmnx[qq])
ax.xaxis.set_major_locator(plt.MultipleLocator(50.))
ax.set_ylim(-0.1, 1.2)
ax.set_ylabel('Normalized Flux')
if jj == 1:
ax.set_xlabel('Relative Velocity (km/s)')
else:
ax.get_xaxis().set_ticks([])
# Plot
velo = spec.relative_vel(itrans * u.AA * (1 + qpq8_zfg[qq]))
ax.plot(velo, spec.flux, color='white', drawstyle='steps')
ax.plot(qpq8_vmnx[qq], [1.] * 2, '--', color='cyan')
# Label
ax.text(0.80,
0.10,
lbls[jj],
transform=ax.transAxes,
size='large',
ha='center',
color='yellow')
# Write
plt.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
print('Genereated {:s}'.format(outfil))
def fig_molecules():
""" H2, Lya, CII plots
"""
# Spec files
# Load QPQ7
#if qpq7 is None:
# qpq7 = equ.load_qpq(7)
# LineList
H2 = LineList('H2')
CO_waves = [1447.3521, 1477.5649, 1509.7480]
CO_lbls = ['CO 2-0', 'CO 1-0', 'CO 0-0']
outfil = 'fig_qpq_molecules.pdf'
pp = PdfPages(outfil)
fig = plt.figure(figsize=(8.5, 4))
plt.clf()
gs = gridspec.GridSpec(2, 5)
xpsimp.dark_bkgd(plt)
qpq8_sys = ['J114436.65+095904.9', 'J142758.73-012136.1']
qpq8_yrng = [(0., 1.2), (0., 1.2)]
wvobs = [(4160, 4240.), (4735, 4950)] # Lyman-Werner, CO
#qpq8_sys = ['J120416.68+022110.9']
qpq8_zfg = [2.973, 2.27616]
trans = [1215.6701, 1334.5323]
tvmnx = [(-400, 400), (-200, 200)]
lbls = ['HI Lya', 'CII 1334']
for qq, qsys in enumerate(qpq8_sys):
# Load spectrum
sdict = eqs.spec_wvobs(qsys, wvobs[qq][0] * u.AA, high_res=2)
spec = sdict['spec']
spec.normalize(sdict['conti'])
if qq == 1: # Smooth for presentation
tmpspec = XSpectrum1D.from_tuple((spec.wavelength, spec.flux))
spec = tmpspec.box_smooth(3)
# Loop on standard transitions
for jj, itrans in enumerate(trans):
ax = plt.subplot(gs[qq, jj])
ax.set_xlim(tvmnx[jj])
ax.xaxis.set_major_locator(plt.MultipleLocator(200.))
ax.set_ylim(-0.05, 1.2)
if jj == 0:
ax.set_ylabel('Flux')
ax.set_xlabel('Velocity (km/s)')
# Plot
velo = spec.relative_vel(itrans * u.AA * (1 + qpq8_zfg[qq]))
ax.plot(velo, spec.flux, color='white', drawstyle='steps')
ax.plot(tvmnx[jj], [1.] * 2, '--', color='lightgreen')
# Label
ax.text(0.50,
0.90,
lbls[jj],
transform=ax.transAxes,
size='large',
ha='center',
color='yellow')
# Molecules
ax = plt.subplot(gs[qq, len(trans):])
ax.set_xlim(wvobs[qq])
ax.set_ylim(qpq8_yrng[qq])
ax.set_xlabel('Wavelength (Angstroms)')
ax.plot(spec.wavelength, spec.flux, color='white', drawstyle='steps')
if qq == 0: # Lyman-Werner
wrlim = [iwv * u.AA / (1 + qpq8_zfg[qq]) for iwv in wvobs[qq]]
gdlin = np.where((H2._fulltable['Jk'] < 7)
& (H2._fulltable['wrest'] > wrlim[0])
& (H2._fulltable['wrest'] < wrlim[1]))[0]
for igd in gdlin:
if H2._fulltable['Jk'][igd] <= 2:
clr = 'cyan'
do_lbl = True
else:
clr = 'gray'
do_lbl = False
ax.plot(
[H2._fulltable['wrest'][igd].value *
(1 + qpq8_zfg[qq])] * 2,
qpq8_yrng[qq],
'--',
color=clr)
if do_lbl:
ax.text(H2._fulltable['wrest'][igd].value *
(1 + qpq8_zfg[qq]),
0.4,
H2._fulltable['name'][igd],
rotation=90.,
color=clr,
size=12)
else: # CO
for jj, CO_wave in enumerate(CO_waves):
ax.plot([CO_wave * (1 + qpq8_zfg[qq])] * 2,
qpq8_yrng[qq],
'--',
color='cyan')
ax.text(CO_wave * (1 + qpq8_zfg[qq]),
0.4,
CO_lbls[jj],
rotation=90,
color='cyan',
size=12)
# Write
plt.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
print('Genereated {:s}'.format(outfil))