def plot_vel_width_sims(sims, snap, log=False):
"""Plot velocity widths for a series of simulations"""
vel_data.plot_prochaska_2008_data()
for sss in sims:
#Make abs. plot
hspec = get_hspec(sss, snap)
hspec.plot_vel_width("Si", 2, color=colors[sss], ls=lss[sss])
outstr = "cosmo_vel_width_z"+str(snap)
if log:
ax = plt.gca()
ax.set_yscale('log')
plt.ylim(5e-2,10)
outstr+="_log"
else:
plt.ylim(1e-2,2)
hspec = get_hspec(5, snap, box=10)
hspec.label=labels["S"]
hspec.plot_vel_width("Si", 2, color=colors["S"], ls="--")
hspec.plot_vw_errors("Si", 2, samples=100,cumulative=False, color=colors2["S"])
plt.xlabel(r"$v_\mathrm{90}$ (km s$^{-1}$)")
# plt.ylabel("Spectra per log interval")
plt.xlim(10,1000)
plt.xticks([10, 100, 1000],["10","100","1000"])
plt.legend(loc=2,ncol=3)
save_figure(path.join(outdir,outstr))
plt.clf()
def do_length_split(cat, subdir):
"""Check the effect of the quasar redshift."""
#Check z_qso split
oldcond = cat.condition
high_z = (0.2, 0.4, 0.6, 0.8, 2)
low_z = (0., 0.2, 0.4, 0.6, 0.8)
z_diff = cat.z_max() - cat.z_min()
for (high_z_qso, z_qso_split) in zip(high_z, low_z):
cat.condition = (z_diff < high_z_qso) * (z_diff > z_qso_split)
cat.plot_omega_dla(label=str(high_z_qso) + " > zQSO > " +
str(z_qso_split))
plt.ylim(ymin=0)
plt.legend(loc=0)
save_figure(path.join(subdir, "omega_gp_zdiff"))
plt.clf()
for (high_z_qso, z_qso_split) in zip(high_z, low_z):
cat.condition = (z_diff < high_z_qso) * (z_diff > z_qso_split)
cat.plot_line_density(label=str(high_z_qso) + " > zQSO > " +
str(z_qso_split))
plt.ylim(ymin=0, ymax=0.1)
plt.legend(loc=0)
save_figure(path.join(subdir, "dndx_gp_zdiff"))
plt.clf()
cat.condition = oldcond
def plot_SivsHI(mets=0.05):
"""
Plot the SiII fraction as a function of density, for some metallicity.
Mets is an array, metallicity as a fraction of solar.
"""
if np.size(mets) == 1:
mets = np.array([mets,])
tab = cc.CloudyTable(3)
#The hydrogen density in atoms/cm^3
dens = np.logspace(-5,2,100)
#Roughly mean DLA metallicity
tabHI = cg.RahmatiRT(3, 0.71)
tempHI = 1e4*np.ones_like(dens)
fracHI = tabHI.neutral_fraction(dens,tempHI)
plt.semilogx(dens, fracHI, color="red",ls="--")
ls = [":","-","-."]
for met in mets:
metSi = tab.get_solar("Si")*met*np.ones_like(dens)
fracSi = tab.ion("Si",2,metSi,dens)
plt.semilogx(dens, fracSi, color="green",ls=ls.pop())
plt.xlabel(r"$\rho_\mathrm{H}\; (\mathrm{amu}/\mathrm{cm}^3$)")
plt.ylabel(r"$\mathrm{m}_\mathrm{SiII} / \mathrm{m}_\mathrm{Si}$")
plt.show()
save_figure(path.join(outdir,"Si_fracs"))
def plot_halo_stellar_mass():
"""Plot a histogram of nearby halos"""
for sim in (1, 7, 9): #xrange(8):
halo = myname.get_name(sim, True)
hms = []
sms = []
sfrs = []
zz = []
for snap in (1, 3, 5):
ahalo = dp.PrettyBox(halo, snap, nslice=10, label=labels[sim])
(hm, sm, sfr) = ahalo.get_avg_stellar_mass()
hms.append(hm)
sms.append(sm)
sfrs.append(sfr)
zz.append(redshifts[snap])
plt.figure(1)
plt.semilogy(zz, hms, color=colors[sim], ls="-", label=labels[sim])
plt.semilogy(zz, sms, color=colors[sim], ls="--", label=labels[sim])
plt.figure(2)
plt.semilogy(zz, sfrs, color=colors[sim], ls="--", label=labels[sim])
plt.figure(1)
plt.legend(loc=1)
save_figure(path.join(outdir, "halos/avg_smhm_z" + str(snap)))
plt.figure(2)
plt.legend(loc=1)
save_figure(path.join(outdir, "halos/avg_sfr_z" + str(snap)))
plt.clf()
def plot_H2_effect(sim, snap):
"""Load a simulation and plot its cddf"""
halo = myname.get_name(sim, True)
savefile = "boxhi_grid_noH2.hdf5"
ahalo = dp.PrettyBox(halo, snap, nslice=10, savefile=savefile, label=r"No $H_2$")
ahalo.plot_column_density(color="blue", ls="--", moment=True)
savefile = "boxhi_grid_H2.hdf5"
ahalo2 = dp.PrettyBox(halo, snap, nslice=10, savefile=savefile, label=r"$H_2$")
ahalo2.plot_column_density(color="red",moment=True)
# savefile = path.join(halo,"snapdir_"+str(snap).rjust(3,'0'),"boxhi_grid_H2-old.hdf5")
# ahalo2 = dp.PrettyBox(halo, snap, nslice=10, savefile=savefile)
# ahalo2.plot_column_density(color="green",moment=True)
dla_data.column_density_data(moment=True)
# dla_data.noterdaeme_12_data(path.join(path.dirname(__file__),"../dla_data"), moment=True)
plt.legend(loc=3)
plt.xlim(1e20,2e22)
plt.ylim(1e-5,0.1)
# plt.title("CDDF for "+labels[sim]+" at z="+str(redshifts[snap]))
save_figure(path.join(outdir, "cosmo"+str(sim)+"_H2_"+str(snap)))
plt.clf()
cddf_base = ahalo.column_density_function()
cddf = ahalo2.column_density_function()
plt.semilogx(cddf_base[0], np.log10(cddf[1]/cddf_base[1]), color=colors[sim], ls=lss[sim])
plt.ylim(-0.5,0.5)
tight_layout_wrapper()
ax = plt.gca()
ylab = ax.set_ylabel(r"$N_\mathrm{HI} f(N)$")
save_figure(path.join(outdir, "cosmo_rel"+str(sim)+"_H2_"+str(snap)))
plt.clf()
def save_plot(elem, ion, suffix, ss_corr=True):
"""Helper function to save a nicely named file"""
filename = elem + str(ion) + "_" + suffix
if ss_corr:
save_figure(path.join(outdir, filename + "_photo_atten"))
else:
save_figure(path.join(outdir, filename + "_no_atten"))
def plot_all_rho(simlist):
"""Make the rho_HI plot with labels etc"""
#Cosmo0
for i in simlist: #xrange(8):
(zzz,dndx,omegadla) = get_rhohi_dndx(i)
plt.figure(1)
plt.plot(zzz,dndx, 'o', color=colors[i], ls=lss[i], label=labels[i])
plt.figure(2)
plt.plot(zzz,omegadla, 'o', color=colors[i], ls=lss[i],label=labels[i])
plt.figure(1)
plt.xlabel("z")
plt.ylabel(r"$dN / dX$")
dla_data.dndx_not()
dla_data.dndx_pro()
plt.xlim(2,4)
plt.ylim(0,0.13)
plt.legend(loc=4, ncol=3)
tight_layout_wrapper()
save_figure(path.join(outdir,"cosmo_dndx"))
plt.clf()
plt.figure(2)
plt.xlabel("z")
plt.ylabel(r"$10^3 \Omega_\mathrm{DLA}$")
dla_data.omegahi_not()
# dla_data.omegahi_pro()
plt.xlim(2,4)
plt.ylim(0,2.)
plt.legend(loc=4, ncol=3)
tight_layout_wrapper()
save_figure(path.join(outdir,"cosmo_rhohi"))
plt.clf()
def plot_dndx_breakdown(sim):
"""Make the rho_HI plot with labels etc"""
halo = myname.get_name(sim, True, 25)
snaps = {4: 1, 3.5: 2, 3: 3, 2.5: 4, 2: 5}
fractions = []
zzz = []
omegadla = []
for zzzz in (4, 3.5, 3, 2.5, 2):
ahalo = dp.PrettyBox(halo, snaps[zzzz], nslice=10)
(massbins, fracs) = ahalo.get_omega_hi_mass_breakdown(False)
fractions.append(fracs)
zzz.append(zzzz)
omegadla.append(ahalo.line_density())
fractions = np.array(fractions)
for i in xrange(np.size(fractions[0, :]) - 2):
plt.plot(zzz,
fractions[:, i + 1],
color=colors[i],
ls=lss[i],
label=dp.pr_num(np.log10(massbins[i])) + " - " +
dp.pr_num(np.log10(massbins[i + 1])))
plt.plot(zzz, fractions[:, -1], color=colors[6], ls=lss[6], label="Field")
plt.plot(zzz, omegadla, color=colors[sim], ls=lss[sim], label="Total")
plt.xlabel("z")
plt.ylabel(r"$dN/dX$")
dla_data.dndx_not()
dla_data.dndx_pro()
plt.xlim(2, 4)
plt.ylim(0, 0.15)
plt.legend(loc=1, ncol=2)
tight_layout_wrapper()
save_figure(path.join(outdir, "cosmo_dndx_break" + str(sim)))
plt.clf()
def plot_halos(sim,hh):
"""Plot the halo closest in mass and position in the given sim to the halo of the given number in sim 7."""
ahalo = dp.PrettyHalo(myname.get_name(sim),3,20000)
ahalo7 = dp.PrettyHalo(myname.get_name(7),3,20000)
(mass, cofm, radii) = _load_halo(ahalo, 30)
(mass7, cofm7, _) = _load_halo(ahalo7, 30)
dist = np.sum((cofm7[hh] - cofm)**2, axis=1)
nn = np.where( dist == np.min(dist))
rhh = hh
hh = np.ravel(nn)[0]
print "Requested: ",rhh,"Got: ",hh," dist:",np.sqrt(dist[nn])," r-mass:",mass[hh]/mass7[rhh], "ormass: ",mass7[rhh]
plt.title(r"Central Halo: $"+dp.pr_num(ahalo.sub_mass[hh]/0.72/1e11)+r"\times 10^{11} M_\odot$")
ahalo.plot_pretty_halo(hh)
#Backwards because someone is a fortran programmer
circle=plt.Circle((0,0),radii[hh],color="black",fill=False)
ax = plt.gca()
ax.add_artist(circle)
# plot_rvir(ahalo.sub_cofm[hh], cofm, radii,ahalo.sub_radii[hh])
dp.tight_layout_wrapper()
save_figure(path.join(outdir,"pretty_"+str(sim)+"_halo_"+str(rhh)))
plt.clf()
ahalo.plot_pretty_cut_halo(hh)
circle=plt.Circle((0,0),radii[hh],color="black",fill=False)
ax = plt.gca()
ax.add_artist(circle)
# plot_rvir(ahalo.sub_cofm[hh], cofm, radii,ahalo.sub_radii[hh]/)
plt.title(labels[sim]+" at z=3")
dp.tight_layout_wrapper()
save_figure(path.join(outdir,"pretty_cut_"+str(sim)+"_halo_"+str(rhh)))
plt.clf()
del ahalo
def plot_dndx_breakdown(sim):
"""Make the rho_HI plot with labels etc"""
halo = myname.get_name(sim, True, 25)
snaps = {4:1, 3.5:2, 3:3, 2.5:4, 2:5}
fractions=[]
zzz = []
omegadla = []
for zzzz in (4, 3.5, 3, 2.5, 2):
ahalo = dp.PrettyBox(halo, snaps[zzzz], nslice=10)
(massbins, fracs) = ahalo.get_omega_hi_mass_breakdown(False)
fractions.append(fracs)
zzz.append(zzzz)
omegadla.append(ahalo.line_density())
fractions = np.array(fractions)
for i in xrange(np.size(fractions[0,:])-2):
plt.plot(zzz,fractions[:,i+1], color=colors[i], ls=lss[i], label=dp.pr_num(np.log10(massbins[i]))+" - "+dp.pr_num(np.log10(massbins[i+1])))
plt.plot(zzz,fractions[:,-1], color=colors[6], ls=lss[6], label="Field")
plt.plot(zzz,omegadla, color=colors[sim], ls=lss[sim], label="Total")
plt.xlabel("z")
plt.ylabel(r"$dN/dX$")
dla_data.dndx_not()
dla_data.dndx_pro()
plt.xlim(2,4)
plt.ylim(0,0.15)
plt.legend(loc=1, ncol=2)
tight_layout_wrapper()
save_figure(path.join(outdir,"cosmo_dndx_break"+str(sim)))
plt.clf()
def plot_halo_stellar_mass():
"""Plot a histogram of nearby halos"""
for sim in (1,7,9): #xrange(8):
halo = myname.get_name(sim, True)
hms = []
sms = []
sfrs = []
zz = []
for snap in (1,3,5):
ahalo = dp.PrettyBox(halo, snap, nslice=10, label=labels[sim])
(hm, sm, sfr) = ahalo.get_avg_stellar_mass()
hms.append(hm)
sms.append(sm)
sfrs.append(sfr)
zz.append(redshifts[snap])
plt.figure(1)
plt.semilogy(zz, hms, color=colors[sim], ls="-", label=labels[sim])
plt.semilogy(zz, sms, color=colors[sim], ls="--", label=labels[sim])
plt.figure(2)
plt.semilogy(zz, sfrs, color=colors[sim], ls="--", label=labels[sim])
plt.figure(1)
plt.legend(loc=1)
save_figure(path.join(outdir, "halos/avg_smhm_z"+str(snap)))
plt.figure(2)
plt.legend(loc=1)
save_figure(path.join(outdir, "halos/avg_sfr_z"+str(snap)))
plt.clf()
def do_snr_check(cat, subdir):
"""Check effect of removing spectra with a low SNR."""
first_snr = cat.snr_thresh
cat.set_snr(-2)
cat.plot_omega_dla(zmax=5, label="All GP")
cat.set_snr(2)
cat.plot_omega_dla(zmax=5, label="SNR > 2")
cat.set_snr(4)
cat.plot_omega_dla(zmax=5, label="SNR > 4")
# cat.set_snr(8)
# cat.plot_omega_dla(zmax=5,label="SNR > 8")
plt.legend(loc=0)
save_figure(path.join(subdir, "omega_gp_snr"))
plt.clf()
cat.set_snr(-2)
cat.plot_line_density(zmax=5, label="All GP")
cat.set_snr(2)
cat.plot_line_density(zmax=5, label="SNR > 2")
cat.set_snr(4)
cat.plot_line_density(zmax=5, label="SNR > 4")
# cat.set_snr(8)
# cat.plot_line_density(zmax=5, label="SNR > 8")
plt.legend(loc=0)
save_figure(path.join(subdir, "dndx_gp_snr"))
plt.clf()
cat.set_snr(first_snr)
def plot_den(sim, snap, num, subdir="", voff = 0, box=10, elem="Si", ion=2):
"""Plot density"""
hspec = get_hspec(sim, snap, snr=20., box=box)
#Adjust the default plot parameters, which do not scale well in a gridspec.
matplotlib.rc('xtick', labelsize=10)
matplotlib.rc('ytick', labelsize=10)
matplotlib.rc('axes', labelsize=10)
matplotlib.rc('font', size=8)
matplotlib.rc('lines', linewidth=1.5)
gs = gridspec.GridSpec(9,2)
ax3 = plt.subplot(gs[0:4,0])
plt.sca(ax3)
xoff = hspec.plot_spectrum(elem,ion,-1,num, flux=False)
xlim = plt.xlim()
ax3.xaxis.set_label_position('top')
ax3.xaxis.tick_top()
voff += xoff
ax2 = plt.subplot(gs[5:,0])
plt.sca(ax2)
dxlim = hspec.plot_density(elem,ion, num)
plt.ylabel(r"n$_\mathrm{"+elem+"II}$ (cm$^{-3}$)")
plt.ylim(ymin=1e-9)
ax1 = plt.subplot(gs[4,0])
plt.sca(ax1)
xscale = dxlim*hspec.velfac/xlim[1]
hspec.plot_den_to_tau(elem, ion, num, thresh = 1e-9, xlim=200,voff=voff, xscale=xscale)
ax1.axes.get_xaxis().set_visible(False)
plt.xlabel("")
plt.xlim(xlim)
sdir = path.join(outdir,"spectra/"+subdir)
if not path.exists(sdir):
os.mkdir(sdir)
save_figure(path.join(sdir,str(num)+"_cosmo"+str(sim)+"_"+elem+"_colden"))
plt.clf()
matplotlib.rc_file_defaults()
def plot_agn_rel_cddf(snap):
"""Load and make a plot of the difference between both simulations with and without AGN"""
basen = myname.get_name(0)
base = dp.PrettyBox(basen, snap, nslice=10)
cddf_base = base.column_density_function()
basen = myname.get_name(4)
other = dp.PrettyBox(basen, snap, nslice=10)
cddf = other.column_density_function()
plt.semilogx(cddf_base[0],
cddf[1] / cddf_base[1],
color=colors[0],
ls=lss[0])
basen = myname.get_name(1)
base = dp.PrettyBox(basen, snap, nslice=10)
cddf_base = base.column_density_function()
basen = myname.get_name(2)
other = dp.PrettyBox(basen, snap, nslice=10)
cddf = other.column_density_function()
plt.semilogx(cddf_base[0],
cddf[1] / cddf_base[1],
color=colors[1],
ls=lss[1])
plt.ylim(0.8, 1.5)
plt.xlim(1e17, 1e22)
save_figure(path.join(outdir, "cosmo_rel_agn_cddf_z" + str(snap)))
plt.clf()
def plot_cum_f_peak_sims(sims, snap):
"""Plot f_peak for a series of simulations"""
(_, cfmm) = vel_data.plot_cum_stat_data(True, None)
norm = cfmm[-1]
for sss in sims:
#Make abs. plot
hspec = get_hspec(sss, snap)
hspec.plot_cum_f_peak("Si",
2,
norm=norm,
color=colors[sss],
ls=lss[sss])
hspec = get_hspec(5, snap, box=10)
hspec.label = labels["S"]
hspec.plot_cum_f_peak("Si", 2, norm=norm, color=colors["S"], ls="--")
hspec.plot_f_peak_errors("Si",
2,
samples=norm,
cumulative=True,
color=colors2["S"])
outstr = "cosmo_cum_f_peak_z" + str(snap)
plt.ylim(0, norm + 1)
plt.ylabel("Cumulative Distribution")
plt.xlim(0, 1)
plt.legend(loc=4, ncol=2)
save_figure(path.join(outdir, outstr))
plt.clf()
def save_plot(elem, ion, suffix, ss_corr=True):
"""Helper function to save a nicely named file"""
filename = elem+str(ion)+"_"+suffix
if ss_corr:
save_figure(path.join(outdir,filename+"_photo_atten"))
else:
save_figure(path.join(outdir,filename+"_no_atten"))
def do_qso_split(cat, subdir):
"""Check the effect of the quasar redshift."""
#Check z_qso split
oldcond = cat.condition
high_z = (2.5, 3.0, 3.5, 5.0)
low_z = (2.0, 2.5, 3.0, 3.5)
for (high_z_qso, z_qso_split) in zip(high_z, low_z):
cat.condition = (cat.z_max() < high_z_qso) * (cat.z_max() >
z_qso_split)
cat.plot_omega_dla(label="$" + str(high_z_qso) +
" > z_\mathrm{QSO} > " + str(z_qso_split) + "$")
plt.ylim(ymin=0)
plt.legend(loc=0)
save_figure(path.join(subdir, "omega_gp_zqso" + str(cat.lowzcut)))
plt.clf()
for (high_z_qso, z_qso_split) in zip(high_z, low_z):
cat.condition = (cat.z_max() < high_z_qso) * (cat.z_max() >
z_qso_split)
cat.plot_line_density(label="$" + str(high_z_qso) +
" > z_\mathrm{QSO} > " + str(z_qso_split) + "$")
plt.ylim(ymin=0, ymax=0.15)
plt.legend(loc=0)
save_figure(path.join(subdir, "dndx_gp_zqso" + str(cat.lowzcut)))
plt.clf()
cat.condition = oldcond
def plot_halos(sim, hh):
"""Plot the halo closest in mass and position in the given sim to the halo of the given number in sim 7."""
ahalo = dp.PrettyHalo(myname.get_name(sim), 3, 20000)
ahalo7 = dp.PrettyHalo(myname.get_name(7), 3, 20000)
(mass, cofm, radii) = _load_halo(ahalo, 30)
(mass7, cofm7, _) = _load_halo(ahalo7, 30)
dist = np.sum((cofm7[hh] - cofm)**2, axis=1)
nn = np.where(dist == np.min(dist))
rhh = hh
hh = np.ravel(nn)[0]
print "Requested: ", rhh, "Got: ", hh, " dist:", np.sqrt(
dist[nn]), " r-mass:", mass[hh] / mass7[rhh], "ormass: ", mass7[rhh]
plt.title(r"Central Halo: $" +
dp.pr_num(ahalo.sub_mass[hh] / 0.72 / 1e11) +
r"\times 10^{11} M_\odot$")
ahalo.plot_pretty_halo(hh)
#Backwards because someone is a fortran programmer
circle = plt.Circle((0, 0), radii[hh], color="black", fill=False)
ax = plt.gca()
ax.add_artist(circle)
# plot_rvir(ahalo.sub_cofm[hh], cofm, radii,ahalo.sub_radii[hh])
dp.tight_layout_wrapper()
save_figure(path.join(outdir, "pretty_" + str(sim) + "_halo_" + str(rhh)))
plt.clf()
ahalo.plot_pretty_cut_halo(hh)
circle = plt.Circle((0, 0), radii[hh], color="black", fill=False)
ax = plt.gca()
ax.add_artist(circle)
# plot_rvir(ahalo.sub_cofm[hh], cofm, radii,ahalo.sub_radii[hh]/)
plt.title(labels[sim] + " at z=3")
dp.tight_layout_wrapper()
save_figure(
path.join(outdir, "pretty_cut_" + str(sim) + "_halo_" + str(rhh)))
plt.clf()
del ahalo
def plot_eq_width(sims, snap):
"""Plot velocity widths for a series of simulations"""
for sss in sims:
#Make abs. plot
hspec = get_hspec(sss, snap)
hspec.plot_eq_width("Si", 2, 1526, color=colors[sss], ls=lss[sss])
hspec = get_hspec(7, snap)
outstr = "cosmo_eq_width_z" + str(snap)
if snap == 5:
nv_table = 7
else:
nv_table = 9
(center, _) = vel_data.plot_si1526_eqw(zrange[snap], nv_table=nv_table)
hspec = get_hspec(5, snap, box=10)
hspec.label = labels["S"]
hspec.plot_eq_width("Si", 2, 1526, color=colors["S"], ls="--")
hspec.plot_eq_width_errors("Si",
2,
1526,
100,
color=colors2["S"],
nv_table=nv_table,
min_width=center[0])
plt.xlabel(r"log $(W_\mathrm{1526} / \AA )$")
plt.ylim(0, 3)
plt.legend(loc=2, ncol=3)
plt.text(-1.3, 2, "z=" + str(zzz[snap]), size=22)
save_figure(path.join(outdir, outstr))
plt.clf()
def plot_vel_width_sims(sims, snap, log=False):
"""Plot velocity widths for a series of simulations"""
vel_data.plot_prochaska_2008_data()
for sss in sims:
#Make abs. plot
hspec = get_hspec(sss, snap)
hspec.plot_vel_width("Si", 2, color=colors[sss], ls=lss[sss])
outstr = "cosmo_vel_width_z" + str(snap)
if log:
ax = plt.gca()
ax.set_yscale('log')
plt.ylim(5e-2, 10)
outstr += "_log"
else:
plt.ylim(1e-2, 2)
hspec = get_hspec(5, snap, box=10)
hspec.label = labels["S"]
hspec.plot_vel_width("Si", 2, color=colors["S"], ls="--")
hspec.plot_vw_errors("Si",
2,
samples=100,
cumulative=False,
color=colors2["S"])
plt.xlabel(r"$v_\mathrm{90}$ (km s$^{-1}$)")
# plt.ylabel("Spectra per log interval")
plt.xlim(10, 1000)
plt.xticks([10, 100, 1000], ["10", "100", "1000"])
plt.legend(loc=2, ncol=3)
save_figure(path.join(outdir, outstr))
plt.clf()
def plot_cum_vel_width_sims(sims, snap):
"""Plot velocity widths for a series of simulations"""
(_, cvels) = vel_data.plot_cum_vw_data(None)
norm = cvels[-1]
for sss in sims:
#Make abs. plot
hspec = get_hspec(sss, snap)
hspec.plot_cum_vel_width("Si",
2,
norm=norm,
color=colors[sss],
ls=lss[sss])
hspec = get_hspec(5, snap, box=10)
hspec.label = labels["S"]
hspec.plot_cum_vel_width("Si", 2, norm=norm, color=colors["S"], ls="--")
hspec.plot_vw_errors("Si",
2,
samples=norm,
cumulative=True,
color=colors2["S"])
outstr = "cosmo_cum_vel_width_z" + str(snap)
plt.ylim(0, norm + 1)
# plt.ylabel("Total Spectra")
plt.xlabel(r"$v_\mathrm{90}$ (km s$^{-1}$)")
plt.xlim(9, 1000)
plt.xticks([10, 100, 1000], ["10", "100", "1000"])
plt.legend(loc=4, ncol=2)
save_figure(path.join(outdir, outstr))
plt.clf()
def test_tescari_halos(sim, snap):
"""Plot velocity width for spectra through the center of halos, like in Tescari 2009"""
halo = myname.get_name(sim, box=10)
hspec = ps.VWPlotSpectra(snap, halo, savefile="halo_spectra_2.hdf5",cdir=path.expanduser("~/codes/cloudy_tables/ion_out_no_atten/"))
hspec.plot_vel_width("Si", 2, color="red")
vel_data.plot_prochaska_2008_data()
save_figure(path.join(outdir,"cosmo_tescari_halos"))
plt.clf()
def plot_covering_frac(sim, snap, ff=True):
"""Load a simulation and plot its cddf"""
halo = myname.get_name(sim, ff)
ahalo = dp.PrettyBox(halo, snap, nslice=10)
ahalo.plot_sigma_DLA()
del ahalo
save_figure(path.join(outdir, "cosmo"+str(sim)+"_covering_z"+str(snap)))
plt.clf()
def plot_UVB_effect():
"""Load a simulation and plot its cddf"""
for i in (0,5,7):
halo = myname.get_name(i, True)
ahalo = dp.PrettyBox(halo, 3, nslice=10)
ahalo.plot_column_density(color=colors[i], ls=lss[i],moment=True)
dla_data.column_density_data(moment=True)
save_figure(path.join(outdir, "cosmo_UVB_3"))
plt.clf()
def plot_UVB_effect():
"""Load a simulation and plot its cddf"""
for i in (0, 5, 7):
halo = myname.get_name(i, True)
ahalo = dp.PrettyBox(halo, 3, nslice=10)
ahalo.plot_column_density(color=colors[i], ls=lss[i], moment=True)
dla_data.column_density_data(moment=True)
save_figure(path.join(outdir, "cosmo_UVB_3"))
plt.clf()
def plot_covering_frac(sim, snap, ff=True):
"""Load a simulation and plot its cddf"""
halo = myname.get_name(sim, ff)
ahalo = dp.PrettyBox(halo, snap, nslice=10)
ahalo.plot_sigma_DLA()
del ahalo
save_figure(
path.join(outdir, "cosmo" + str(sim) + "_covering_z" + str(snap)))
plt.clf()
def mass_hist(name, ahalos):
"""Plot a histogram of halo masses"""
for ahalo in ahalos:
ahalo.plot_mass_hist()
plt.xlabel(r"Halo mass ($M_\odot$)")
plt.ylabel(r"PDF")
plt.ylim(0, 1.5)
plt.legend()
save_figure(path.join(outdir,name+"_CIV_mass_hist"))
plt.clf()
def CIV_eq_ratio(name, ahalos):
"""Carbon IV equivalent width ratio"""
for ahalo in ahalos:
ahalo.plot_eq_width_ratio()
plt.xlabel("r perp (kpc)")
plt.ylabel(r"$\eta_\mathrm{pair} / \eta_\mathrm{DLA}$")
plt.ylim(0, 1.5)
plt.legend()
save_figure(path.join(outdir,name+"_CIV_eq_ratio"))
plt.clf()
def collis_dist(name, ahalos):
"""Plot the collisional ionisation fractions"""
for ahalo in ahalos:
ahalo.plot_collisional_fraction()
plt.xlabel("r perp (kpc)")
plt.ylabel(r"Collisional ionisation fraction")
plt.ylim(0, 1.5)
plt.legend()
save_figure(path.join(outdir,name+"_CIV_collisional"))
plt.clf()
def C_ionic_eq_width(name, ahalo):
"""Plot eq. width distribution"""
ahalo.plot_eq_width(elem="C", ion=4, line=1548,color="grey",label="C-IV")
ahalo.plot_eq_width(elem="C", ion=-1, line=1548, color="pink", label="C-ALL")
plt.xlabel("r perp (kpc)")
plt.ylabel(r"EW(CIV 1548)")
CGM_w = np.loadtxt("CGMofDLAs_avgWCIV.dat")
plt.errorbar(CGM_w[:,0], CGM_w[:,1], yerr = CGM_w[:,2], xerr=[CGM_w[:,0]-[0,7,100,200],[7,100,200,275]-CGM_w[:,0]], fmt='o',ecolor="black")
save_figure(path.join(outdir,name+"_CIV_eq_width"))
plt.clf()
def plot_metallicity(sims, snap):
"""Plot metallicity, vel width, their correlation and the extra statistics"""
out = "cosmo_metallicity_z" + str(snap)
for sim in sims:
hspec = get_hspec(sim, snap)
hspec.plot_metallicity(color=colors[sim], ls=lss[sim])
vel_data.plot_alpha_metal_data(zrange[snap])
plt.legend(loc=2, ncol=3)
plt.ylim(0, 2)
save_figure(path.join(outdir, out))
plt.clf()
def plot_metallicity(sims, snap):
"""Plot metallicity, vel width, their correlation and the extra statistics"""
out = "cosmo_metallicity_z"+str(snap)
for sim in sims:
hspec = get_hspec(sim, snap)
hspec.plot_metallicity(color=colors[sim], ls=lss[sim])
vel_data.plot_alpha_metal_data(zrange[snap])
plt.legend(loc=2,ncol=3)
plt.ylim(0,2)
save_figure(path.join(outdir,out))
plt.clf()
def rel_c_colden(ahalo):
"""Column density for different carbon ions"""
ahalo.plot_colden_ratio(color="grey",elem="C",ion=4,ion2=-1, label="CIV")
ahalo.plot_colden_ratio(color="pink",elem="C",ion=2, ion2=-1, label="CII")
ahalo.plot_colden_ratio(color="green",elem="C",ion=3, ion2=-1, label="CIII")
ahalo.plot_colden_ratio(color="blue",elem="C",ion=5, ion2=-1, label="CV")
#(center, mean_plot_arr6) = ahalo.plot_colden_ratio(color="yellow",elem="C",ion=6, ion2=-1, label="CVI")
#(center, mean_plot_arr7) = ahalo.plot_colden_ratio(color="red",elem="C",ion=7, ion2=-1, label="CVII")
#plt.plot(center, mean_plot_arr2+mean_plot_arr3+mean_plot_arr4+mean_plot_arr5+mean_plot_arr6+mean_plot_arr7, color="black")
plt.legend(loc='upper center', ncol=2)
save_figure(path.join(outdir,"ion_C_colden_ratio"))
plt.clf()
def do_check_p_thresh(cat, subdir):
"""Check the effect of very unlikely samples"""
cat.p_thresh_sample = 1e-4
cat.plot_line_density(zmax=5, label=r"$p_\mathrm{sample} = 10^{-4}$")
cat.p_thresh_sample = 1e-2
cat.plot_line_density(zmax=5, label=r"$p_\mathrm{sample} = 10^{-2}$")
cat.p_thresh_sample = 1e-4
cat.p_thresh_spec = 0.1
cat.plot_line_density(zmax=5, label=r"$p_\mathrm{spec} = 10^{-1}$")
plt.legend(loc=0)
save_figure(path.join(subdir, "dndx_p_thresh"))
plt.clf()
def C_ionic_coverfrac(name, ahalo):
"""Plot covering fraction"""
ahalo.plot_covering_fraction(elem="C", ion=4, line=1548,color="grey",label="C-IV")
ahalo.plot_covering_fraction(elem="C", ion=-1, line=1548, color="pink", label="C-ALL")
plt.xlabel("r perp (kpc)")
plt.ylabel(r"$F(W_{1548} > 0.2 \AA)$")
CGM_c = np.loadtxt("CGMofDLAs_CfCIV.dat")
plt.errorbar(CGM_c[:,0], CGM_c[:,2], yerr = [CGM_c[:,2]-CGM_c[:,1],CGM_c[:,3]-CGM_c[:,2]], fmt='o', xerr=[CGM_c[:,0]-[7,100,200],[100,200,275]-CGM_c[:,0]],ecolor="black")
plt.ylim(0,1.0)
plt.legend()
save_figure(path.join(outdir,name+"_CIV_coverfrac"))
plt.clf()
def HI_coverfrac(name, ahalos):
"""CIV covering fraction"""
for ahalo in ahalos:
ahalo.plot_covering_fraction_colden(elem="H", ion=1)
plt.xlabel("r perp (kpc)")
plt.ylabel(r"$F(LLS)$")
CGM_c = np.loadtxt("CGMofDLAs_Cfothick.dat")
plt.errorbar(CGM_c[:,0], CGM_c[:,2], yerr = [CGM_c[:,2]-CGM_c[:,1],CGM_c[:,3]-CGM_c[:,2]], fmt='o', xerr=[CGM_c[:,0]-[7,50,117.5,200],[50,117.5,200,275]-CGM_c[:,0]],ecolor="black")
plt.ylim(0,1.0)
plt.legend()
save_figure(path.join(outdir,name+"_LLS_coverfrac"))
plt.clf()
def test_tescari_halos(sim, snap):
"""Plot velocity width for spectra through the center of halos, like in Tescari 2009"""
halo = myname.get_name(sim, box=10)
hspec = ps.VWPlotSpectra(
snap,
halo,
savefile="halo_spectra_2.hdf5",
cdir=path.expanduser("~/codes/cloudy_tables/ion_out_no_atten/"))
hspec.plot_vel_width("Si", 2, color="red")
vel_data.plot_prochaska_2008_data()
save_figure(path.join(outdir, "cosmo_tescari_halos"))
plt.clf()
def plot_vel_widths_metal():
"""Plot some velocity width data at a particular redshift"""
#Load sims
colorss = {1: "blue", 4: "purple", 3: "orange", 5: "red"}
for sim in (1, 4, 5):
halo = "modified_128_a" + str(sim) + "_b1"
hspec0 = ps.VWPlotSpectra(25, base + halo)
#Make abs. plot
hspec0.plot_vel_width("Si", 2, color=colorss[sim], ls="-")
vel_data.plot_prochaska_2008_data()
save_figure(path.join(outdir, "cosmo_velw_metal_load"))
plt.clf()
def generic_coverfrac(ionname, elem, ion, line, name, ahalos):
"""Plot covering fraction"""
for ahalo in ahalos:
ahalo.plot_covering_fraction(elem=elem, ion=ion, line=line)
plt.xlabel("r perp (kpc)")
plt.ylabel(r"$F(W_{"+str(line)+r"} > 0.2 \AA)$")
CGM_c = np.loadtxt("CGMofDLAs_Cf"+ionname+".dat")
plt.errorbar(CGM_c[:,0], CGM_c[:,2], yerr = [CGM_c[:,2]-CGM_c[:,1],CGM_c[:,3]-CGM_c[:,2]], fmt='o', xerr=[CGM_c[:,0]-[7,100,200],[100,200,275]-CGM_c[:,0]],ecolor="black")
plt.ylim(0,1.0)
plt.legend()
save_figure(path.join(outdir,name+"_"+ionname+"_coverfrac"))
plt.clf()
def plot_vel_widths_metal():
"""Plot some velocity width data at a particular redshift"""
#Load sims
colorss={1:"blue", 4:"purple", 3:"orange", 5:"red"}
for sim in (1,4,5):
halo = "modified_128_a"+str(sim)+"_b1"
hspec0 = ps.VWPlotSpectra(25, base+halo)
#Make abs. plot
hspec0.plot_vel_width("Si", 2, color=colorss[sim], ls="-")
vel_data.plot_prochaska_2008_data()
save_figure(path.join(outdir,"cosmo_velw_metal_load"))
plt.clf()
def plot_metal_ion_corr(sim, snap,species="Si",ion=2):
"""Plot metallicity from Z/H vs from a single species for computing ionisation corrections"""
halo = myname.get_name(sim)
hspec = ps.VWPlotSpectra(snap, halo)
hspec.plot_metallicity(color="red", ls="-")
hspec.plot_species_metallicity(species, ion, color="blue", ls="-")
vel_data.plot_alpha_metal_data((3.5,2.5))
save_figure(path.join(outdir, "cosmo_metallicity"+str(sim)+"_ion_corr"+str(snap)))
plt.clf()
hspec.plot_ion_corr(species, ion)
save_figure(path.join(outdir, "cosmo_metallicity"+str(sim)+"_rel_ion_corr"+str(snap)))
plt.clf()
def plot_covering_frac(sim, snap, ff=True):
"""Load a simulation and plot its cddf"""
halo = "Cosmo"+str(sim)+"_V6"
if ff:
halo+="_512"
ahalo = dp.PrettyBox(base+halo, snap, nslice=10)
ahalo.plot_sigma_DLA()
save_figure(path.join(outdir, "cosmo"+str(sim)+"_covering_z"+str(snap)))
plt.clf()
ahalo.plot_halo_hist()
save_figure(path.join(outdir, "cosmo"+str(sim)+"_halohist_z"+str(snap)))
del ahalo
plt.clf()
def do_sample_error_check(cat, subdir):
"""Do a bunch of resamplings to check the effect of sample variance."""
#dNdX/Omega_DLA
cat.plot_dndx_sample_errors(z_max=5, nsample=13)
plt.legend(loc=0)
plt.ylim(0, 0.16)
save_figure(path.join(subdir, "dndx_gp_resample"))
plt.clf()
cat.plot_omega_sample_errors(z_max=5, nsample=13)
plt.legend(loc=0)
plt.ylim(0, 2.5)
save_figure(path.join(subdir, "omega_gp_resample"))
plt.clf()
def CIV_vel_offset(name, ahalos):
"""Velocity offset of CIV from the DLAs"""
vel_offset_rubin()
for ahalo in ahalos:
ahalo.plot_flux_vel_offset()
plt.ylabel("N")
plt.xlabel(r"$v_\mathrm{pair} - v_\mathrm{DLA}$ (km/s)")
plt.ylim(0,4)
plt.xlim(0,120)
plt.yticks(np.arange(0,5),("0","1","2","3","4"))
plt.legend()
save_figure(path.join(outdir,name+"_CIV_vel_offset"))
plt.clf()
def plot_breakdown(simlist):
"""Make a plot of the column density function, broken down by halo mass."""
for sss in simlist:
halo = myname.get_name(sss, True)
for nn in (1,3,5):
ahalo = dp.PrettyBox(halo, nn, nslice=10)
ahalo.plot_colden_mass_breakdown()
plt.xlim(20.3,22.3)
plt.ylim(0,1.4)
plt.legend(loc=2,ncol=2)
save_figure(path.join(outdir,"halos/break/cosmo"+str(sss)+"_"+str(nn)+"_break"))
plt.clf()
del ahalo
def plot_rel_vel_width(sims, snap):
"""Plot velocity widths relative to simulation 7"""
hspec = get_hspec(7, snap)
(vbin, vels7) = hspec.vel_width_hist("Si", 2)
#Make rel plot
for sss in sims:
hspec = get_hspec(sss, snap)
(vbin, vel) = hspec.vel_width_hist("Si", 2)
mm = np.min([np.size(vel), np.size(vels7)])
plt.semilogx(vbin[:mm], vel[:mm]/vels7[:mm], color=colors[sss],ls=lss[sss])
plt.xlim(10, 1000)
save_figure(path.join(outdir,"cosmo_rel_vel_z"+str(snap)))
plt.clf()
def plot_vir_vsmass(sim, snap):
"""Plot mass histogram"""
#Load from a save file only
hspec = get_hspec(sim, snap)
(halos, _) = hspec.find_nearest_halo()
hspec._plot_xx_vs_mass(hspec.sub_mass[halos] + 1,
name="Mass",
color=colors[sim],
color2=colors2[sim],
log=True)
out = "cosmo" + str(sim) + "_vir_mass_z" + str(snap)
save_figure(path.join(outdir, out))
plt.clf()
def do_halomass_plots(fosc):
"""Plot halo mass, distance to the halo and the relationship between eq. width and column density"""
ahalos = {
4:CIVPlottingSpectra(5, myname.get_name(4, box=25), None, None, savefile="rand_civ_spectra.hdf5", spec_res=5.,label=labels[4]+" 25"),
9:CIVPlottingSpectra(5, myname.get_name(9, box=25), None, None, savefile="rand_civ_spectra.hdf5", spec_res=5.,label=labels[9]+" 25"),
7:CIVPlottingSpectra(5, myname.get_name(7, box=25), None, None, savefile="rand_civ_spectra.hdf5", spec_res=5.,label=labels[7]+" 25")}
for (ll, ahalo) in ahalos.items():
ahalo.plot_eqw_mass("C",4,1548,color=colors[ll])
plt.legend(loc="upper left")
save_figure(path.join(outdir,"civ_eqwvsmass"))
plt.clf()
for (ll, ahalo) in ahalos.items():
ahalo.plot_eqw_dist("C",4,1548,color=colors[ll])
plt.legend(loc="upper left")
save_figure(path.join(outdir,"civ_eqwvsdist"))
plt.clf()
ahalos['I']=CIVPlottingSpectra(68, path.expanduser("~/data/Illustris"), None, None, savefile="rand_civ_spectra.hdf5", spec_res=5.,label=labels['I']+" 75")
ccc = {1e12: "yellow", 1e15:"red"}
for tag in ('I', 4, 7):
for nmin in (1e12, 1e15):
nminstr = str(np.round(np.log10(nmin),1))
#for (ll, ahalo) in ahalos.iteritems():
ahalos[tag].plot_mass_hist(elem="C",ion=4,color=ccc[nmin], ls=lss[tag],nmin=nmin, label=ahalos[tag].label+" "+nminstr)
plt.legend(loc="upper left",ncol=1)
save_figure(path.join(outdir,"civ_halos_hist"))
plt.clf()
ahalos['I'].plot_eq_width_vs_col_den("C",4,1548)
eqw = np.linspace(-3, 0.5,50)
plt.semilogy(eqw, linear_cog_col(10**eqw, 1548, fosc), '-',color="black")
plt.ylim(1e12,1e16)
plt.xlim(-2.5,0.5)
save_figure(path.join(outdir,"civ_eqwvscolden"))
plt.clf()
def hc_tau_par(ahalo, name="ion", ions=(2,3,4,5,-1)):
"""Plot the column densities for different CIV ions"""
if 2 in ions:
ahalo.plot_tau_par(color="deeppink",ls="-.",elem="C",ion=2,line=1334,label="CII")
if 4 in ions:
ahalo.plot_tau_par(color="grey",ls="--", elem="C",ion=4,line=1548,label="CIV")
#ahalo.plot_colden(color="black",elem="H",ion=1,label="HI")
plt.yscale('log')
plt.ylabel(r"Optical Depth")
plt.xlabel(r"Velocity from DLA (kms$^{-1}$)")
plt.ylim(0.1, 100)
plt.legend(loc='upper right', ncol=3)
save_figure(path.join(outdir,name+"_C_tau_par"+ahalo.label.replace(" ","_")))
plt.clf()
def plot_vw_break(sim, snap):
"""Plot breakdown of velocity width by halo mass"""
hspec = get_hspec(sim, snap)
hspec.plot_vel_width_breakdown()
out = "cosmo" + str(sim) + "_vw_break_z" + str(snap)
plt.legend(loc=1, ncol=3)
plt.xlim(8, 700)
plt.xticks((10, 40, 100, 400), ("10", "40", "100", "400"))
save_figure(path.join(topdir, out))
plt.clf()
hspec.plot_f_peak_breakdown()
out = "cosmo" + str(sim) + "_fedge_break_z" + str(snap)
save_figure(path.join(topdir, out))
plt.clf()
def plot_H2_effect(sim, snap):
"""Load a simulation and plot its cddf"""
halo = "Cosmo"+str(sim)+"_V6_512"
savefile = path.join(base+halo,"snapdir_"+str(snap).rjust(3,'0'),"boxhi_grid.hdf5")
ahalo = dp.PrettyBox(base+halo, snap, nslice=10, savefile=savefile)
ahalo.plot_column_density(color="blue", ls="--")
del ahalo
savefile = path.join(base+halo,"snapdir_"+str(snap).rjust(3,'0'),"boxhi_grid_H2.hdf5")
ahalo = dp.PrettyBox(base+halo, snap, nslice=10, savefile=savefile)
ahalo.plot_column_density(color="red")
dla_data.column_density_data()
del ahalo
save_figure(path.join(outdir, "cosmo"+str(sim)+"_H2_"+str(snap)))
plt.clf()
def plot_vel_widths_sims(sim):
"""Plot some velocity width data at a particular redshift"""
#Load sims
halo = "modified_128_a" + str(sim) + "_b1"
hspec0 = ps.VWPlotSpectra(17, base + halo)
hspec2 = ps.VWPlotSpectra(25, base + halo)
hspec3 = ps.VWPlotSpectra(36, base + halo)
#Make abs. plot
hspec0.plot_vel_width("Si", 2, color="blue", ls="-")
hspec2.plot_vel_width("Si", 2, color="orange", ls="--")
hspec3.plot_vel_width("Si", 2, color="red", ls="-.")
vel_data.plot_prochaska_2008_data()
save_figure(path.join(outdir, "cosmo_velw_" + str(sim) + "_metal_zz"))
plt.clf()
def plot_rel_vel_width(sims, snap):
"""Plot velocity widths relative to simulation 7"""
hspec = get_hspec(7, snap)
(vbin, vels7) = hspec.vel_width_hist("Si", 2)
#Make rel plot
for sss in sims:
hspec = get_hspec(sss, snap)
(vbin, vel) = hspec.vel_width_hist("Si", 2)
mm = np.min([np.size(vel), np.size(vels7)])
plt.semilogx(vbin[:mm],
vel[:mm] / vels7[:mm],
color=colors[sss],
ls=lss[sss])
plt.xlim(10, 1000)
save_figure(path.join(outdir, "cosmo_rel_vel_z" + str(snap)))
plt.clf()
def plot_metal_ion_corr(sim, snap, species="Si", ion=2):
"""Plot metallicity from Z/H vs from a single species for computing ionisation corrections"""
halo = myname.get_name(sim)
hspec = ps.VWPlotSpectra(snap, halo)
hspec.plot_metallicity(color="red", ls="-")
hspec.plot_species_metallicity(species, ion, color="blue", ls="-")
vel_data.plot_alpha_metal_data((3.5, 2.5))
save_figure(
path.join(outdir,
"cosmo_metallicity" + str(sim) + "_ion_corr" + str(snap)))
plt.clf()
hspec.plot_ion_corr(species, ion)
save_figure(
path.join(outdir, "cosmo_metallicity" + str(sim) + "_rel_ion_corr" +
str(snap)))
plt.clf()
def plot_corr_as_points():
"""Plot the correlation as points"""
halo = myname.get_name(7)
hspec = ps.VWPlotSpectra(3, halo)
vel = hspec.vel_width("Si", 2)
met = hspec.get_metallicity()
#Ignore objects too faint to be seen
ind2 = np.where(met > 1e-4)
met = met[ind2]
vel = vel[ind2]
plt.loglog(vel, met, 'o', color="blue")
plt.xlim(10, 2e3)
plt.ylabel(r"$\mathrm{Z} / \mathrm{Z}_\odot$")
plt.xlabel(r"$v_\mathrm{90}$ (km s$^{-1}$)")
save_figure(path.join(outdir, "cosmo_corr_as_points"))
plt.clf()
def plot_breakdown(simlist):
"""Make a plot of the column density function, broken down by halo mass."""
for sss in simlist:
halo = myname.get_name(sss, True)
for nn in (1, 3, 5):
ahalo = dp.PrettyBox(halo, nn, nslice=10)
ahalo.plot_colden_mass_breakdown()
plt.xlim(20.3, 22.3)
plt.ylim(0, 1.4)
plt.legend(loc=2, ncol=2)
save_figure(
path.join(
outdir,
"halos/break/cosmo" + str(sss) + "_" + str(nn) + "_break"))
plt.clf()
del ahalo
def plot_v_struct(sims, snap):
"""Plot mean-median statistic for all sims on one plot"""
#Plot extra statistics
for sss in sims:
halo = myname.get_name(sss, True)
#Load from a save file only
hspec = RotationFiltered(snap, halo, label=labels[sss], spec_res=0.1)
hspec.get_observer_tau("Si", 2, force_recompute=True)
hspec.plot_vel_width("Si", 2, color=colors[sss], ls=lss[sss])
vel_data.plot_prochaska_2008_data()
plt.legend(loc=2, ncol=3)
plt.xlabel(r"$v_\mathrm{90}$ (km s$^{-1}$)")
plt.xlim(2, 1000)
plt.ylim(0, 2)
save_figure(path.join(outdir, "cosmo_rot_z" + str(snap)))
plt.clf()
def plot_metallicity(sim, snap):
"""Plot a spectrum"""
halo = "modified_128_a" + str(sim) + "_b1"
out = "cosmo" + str(sim) + "_metallicity_z" + str(snap)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, base + halo, None, None)
hspec.plot_metallicity()
vel_data.plot_alpha_metal_data(zrange[snap])
save_figure(path.join(outdir, out))
plt.clf()
out = "cosmo" + str(sim) + "_correlation_z" + str(snap)
hspec.plot_Z_vs_vel_width()
vel_data.plot_prochaska_2008_correlation()
save_figure(path.join(outdir, out))
hspec.save_file()
plt.clf()
def plot_test():
"""Test which plots the neutral fraction for a bunch of particles"""
# plot_file(True,5)
# save_figure.save_figure("test_cold_gas5_molec")
# plt.clf()
#
# plot_file(False,5)
# save_figure.save_figure("test_cold_gas5_no_molec")
# plt.clf()
plot_neut_sim(False, 1)
plt.semilogx(np.ones(3) * 0.168, (0.0, 0.5, 1), "-")
# plt.xticks((0.1,0.15,0.2,0.25))
# plt.xlim(0.1,0.3)
save_figure.save_figure("test_cold_gas1_no_molec")
plt.clf()
