def test_spec_resolution():
"""Plot the velocity widths for different spectral resolutions"""
halo = myname.get_name(7)
#Higher resolution spectrum
hspec = ps.VWPlotSpectra(3, halo, savefile="grid_spectra_DLA.hdf5")
hspec2 = ps.VWPlotSpectra(3, halo, savefile="grid_spectra_DLA_res.hdf5")
plot_check(hspec, hspec2, "specres")
def test_big_box():
"""Plot the velocity widths for different size boxes"""
halo = myname.get_name(0)
halobig = path.expanduser("~/data/Illustris")
hspec = ps.VWPlotSpectra(3, halo, label="DEF")
hspec2 = ps.VWPlotSpectra(59, halobig, label="ILLUS")
plot_check(hspec, hspec2, "bigbox")
def test_min_wind():
"""Plot the velocity widths for minimum wind velocity"""
halo = myname.get_name(7)
halo10 = myname.get_name(5)
zz = 3
hspec = ps.VWPlotSpectra(zz, halo, label="DEF")
hspec2 = ps.VWPlotSpectra(zz, halo10, label="SLIKE")
plot_check(hspec, hspec2, "minwind", zz)
def test_shield():
"""Plot velocity width for spectra using self-shielding like in Tescari 2009"""
halo = myname.get_name(7)
hspec = ps.VWPlotSpectra(3, halo)
hspec2 = ps.VWPlotSpectra(3,
halo,
savefile="grid_spectra_DLA_noshield.hdf5")
plot_check(hspec, hspec2, "no_shield")
def test_vel_abswidth():
"""Plot the velocity widths for different minimum absorber widths"""
halo = myname.get_name(7)
#Higher resolution spectrum
hspec = ps.VWPlotSpectra(3, halo)
hspec2 = ps.VWPlotSpectra(3, halo)
hspec2.minwidth = 250.
plot_check(hspec, hspec2, "abswidth")
def test_metal():
"""Plot the velocity widths for metal enrichment"""
halo = myname.get_name(7)
halo10 = myname.get_name(8)
zz = 3
hspec = ps.VWPlotSpectra(zz, halo, label="DEF")
hspec2 = ps.VWPlotSpectra(zz, halo10, label="ENRICH")
plot_check(hspec, hspec2, "enrich", zz)
def test_box_resolution():
"""Plot the velocity widths for different size boxes"""
halo = myname.get_name(7)
halo10 = myname.get_name(5, box=10)
# for zz in (1,3,5):
zz = 3
hspec = ps.VWPlotSpectra(zz, halo, label="DEF")
hspec2 = ps.VWPlotSpectra(zz, halo10, label="SMALL")
plot_check(hspec, hspec2, "box", zz)
def test_atten():
"""Plot the effect of the self-shielding correction"""
halo = myname.get_name(7)
hspec = ps.VWPlotSpectra(3, halo, label="ATTEN")
hspec2 = ps.VWPlotSpectra(3,
halo,
savefile="grid_spectra_DLA_no_atten.hdf5",
label="NOATTEN")
plot_check(hspec, hspec2, "no_atten")
def test_gfm_shield():
"""Plot the velocity widths for dynamical self-shielding vs post-processed self-shielding."""
halo = myname.get_name(7)
halo2 = myname.get_name('B')
hspec = ps.VWPlotSpectra(3, halo, label="2xUV")
hspec2 = ps.VWPlotSpectra(3, halo2, label="NOSHIELD")
plot_check(hspec, hspec2, "gfm_shield")
hspec = ps.VWPlotSpectra(5, halo, label="2xUV")
hspec2 = ps.VWPlotSpectra(5, halo2, label="NOSHIELD")
plot_check(hspec, hspec2, "gfm_shield", snap=5)
def plot_vel_width_SiII_keating(sim, snap):
"""
Plot the change in velocity widths between the full calculation and
setting n(Si+)/n(Si) = n(HI)/n(H)
"""
halo = myname.get_name(sim)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, halo)
hspecSi2 = ps.VWPlotSpectra(snap, halo, savefile="si_colden_spectra.hdf5")
plot_check(hspec, hspecSi2, "SiHI_keating")
def test_tophat():
"""Plot the velocity widths with and with top hat vs SPH"""
halo = myname.get_name(7)
#Higher resolution spectrum
hspec = ps.VWPlotSpectra(3, halo, savefile="grid_spectra_DLA.hdf5")
hspec2 = ps.VWPlotSpectra(3,
halo,
None,
None,
savefile="grid_spectra_DLA_tophat.hdf5")
plot_check(hspec, hspec2, "tophat")
def test_pecvel():
"""Plot the velocity widths with and without peculiar velocities"""
halo = myname.get_name(7)
#Higher resolution spectrum
hspec = ps.VWPlotSpectra(3, halo, savefile="grid_spectra_DLA.hdf5")
hspec2 = ps.VWPlotSpectra(3,
halo,
None,
None,
savefile="grid_spectra_DLA_pecvel.hdf5")
plot_check(hspec, hspec2, "pecvel")
def test_lowres():
"""Plot the velocity widths with and with top hat vs SPH"""
halo = myname.get_name(0)
halolow = myname.get_name(0, ff=False)
#Higher resolution spectrum
hspec = ps.VWPlotSpectra(3, halo, savefile="grid_spectra_DLA.hdf5")
hspec2 = ps.VWPlotSpectra(60,
halolow,
None,
None,
savefile="rand_spectra_DLA.hdf5")
plot_check(hspec, hspec2, "lowres")
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_vel_width_SiII(sim, snap):
"""
Plot the change in velocity widths between the full calculation and
setting n(Si+)/n(Si) = n(HI)/n(H)
"""
#Load from a save file only
halo = myname.get_name(5, box=10)
hspec_tesc = ps.VWPlotSpectra(
snap, halo, savefile="halo_spectra_2.hdf5"
) #,cdir=path.expanduser("~/codes/cloudy_tables/ion_out_no_atten/"))
hspec_tesc.plot_vel_width("Si", 2, color="green", ls="-.")
halo = myname.get_name(sim)
hspec = ps.VWPlotSpectra(snap, halo)
hspecSi = ps.VWPlotSpectra(snap, halo, savefile="SiHI_spectra.hdf5")
plot_check(hspec, hspecSi, "SiHI")
def get_hspec(sim, snap, box=25):
"""Get a spectra object, possibly from the cache"""
halo = myname.get_name(sim, True, box=box)
#Load from a save file only
try:
hspec = hspec_cache[(halo, snap)]
except KeyError:
hspec = ps.VWPlotSpectra(snap, halo, label=labels[sim])
hspec_cache[(halo, snap)] = hspec
return hspec
def plot_vel_widths_cloudy():
"""Plot some velocity width data for different cloudy models"""
#Load sims
hspec0 = ps.VWPlotSpectra(3, myname.get_name(0, True))
hspec1 = ps.VWPlotSpectra(3,
myname.get_name(0, True),
savefile="rand_spectra_DLA_fancy_atten.hdf5")
#Make abs. plot
hspec0.plot_vel_width("Si", 2, color="blue", ls="--")
hspec1.plot_vel_width("Si", 2, color="red", ls="-")
vel_data.plot_prochaska_2008_data()
save_figure(path.join(outdir, "cosmo_feedback_cloudy_z3"))
plt.clf()
#Make rel plot
(vbin, vels0) = hspec0.vel_width_hist("Si", 2)
(vbin, vels2) = hspec1.vel_width_hist("Si", 2)
mm = np.min((np.size(vels2), np.size(vels0)))
plt.semilogx(vbin[:mm], vels0[:mm] / vels2[:mm], color="blue", ls="-")
plt.xlim(1, 1000)
save_figure(path.join(outdir, "cosmo_rel_vel_cloudy_z3"))
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 plot_vel_metals(sim, snap, ff=True):
"""Plot the correlation between metallicity and velocity width"""
halo = myname.get_name(sim, ff)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, halo)
met = hspec.get_metallicity()
vel = hspec.vel_width("Si", 2)
(H, xedges, yedges) = np.histogram2d(np.log10(met),
np.log10(vel),
bins=30,
normed=True)
extent = [yedges[0], yedges[-1], xedges[-1], xedges[0]]
plt.imshow(H, extent=extent, aspect="auto")
plt.colorbar()
def plot_max_den(sim, snap, ff=True):
"""Load a simulation and plot the max metal density vs the max HI density"""
halo = myname.get_name(sim, ff)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, halo, None, None)
metal_den = np.max(hspec.get_density("Si", 2), axis=1)
HI_den = np.max(hspec.get_density("H", 1), axis=1)
ind = hspec.get_filt("Si", 2)
(H, xedges, yedges) = np.histogram2d(np.log10(metal_den[ind]),
np.log10(HI_den[ind]),
bins=30,
normed=True)
extent = [yedges[0], yedges[-1], xedges[-1], xedges[0]]
plt.imshow(H, extent=extent, aspect="auto", vmax=0.15)
plt.colorbar()
def plot_vel_HI_col_den(sim, snap, ff=True):
"""Load a simulation and plot the HI column density vs the velocity width"""
halo = myname.get_name(sim, ff)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, halo, None, None)
HI_den = np.sum(hspec.get_col_density("H", 1), axis=1)
vel = hspec.vel_width("Si", 2)
ind = hspec.get_filt("Si", 2)
(H, xedges, yedges) = np.histogram2d(np.log10(HI_den[ind]),
np.log10(vel[ind]),
bins=30,
normed=True)
extent = [yedges[0], yedges[-1], xedges[-1], xedges[0]]
plt.imshow(H, extent=extent, aspect="auto")
plt.colorbar()
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_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_met_mass(sim, snap, ff=True):
"""Load a simulation and plot the halo mass vs the velocity width"""
halo = myname.get_name(sim, ff)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, halo)
ind = hspec.get_filt("Si", 2)
met = hspec.get_metallicity()[ind]
(halos, _) = hspec.find_nearest_halo()
mass = hspec.sub_mass[halos][ind]
(H, xedges, yedges) = np.histogram2d(np.log10(mass),
np.log10(met),
bins=30,
normed=True)
extent = [yedges[0], yedges[-1], xedges[-1], xedges[0]]
plt.imshow(H, extent=extent, aspect="auto")
plt.colorbar()
def plot_Si_metals(sim, snap, ff=True):
"""Plot the correlation between metallicity and velocity width"""
halo = myname.get_name(sim, ff)
#Load from a save file only
hspec = ps.VWPlotSpectra(snap, halo)
met = hspec.get_metallicity()
MM = hspec.get_density("Si", 2)
HH = hspec.get_density("H", -1)
mms = np.sum(MM, axis=1)
hhs = np.sum(HH, axis=1)
Simet = mms / hhs / 0.0133
(H, xedges, yedges) = np.histogram2d(np.log10(met),
np.log10(Simet),
bins=30,
normed=True)
extent = [yedges[0], yedges[-1], xedges[-1], xedges[0]]
plt.imshow(H, extent=extent, aspect="auto")
plt.colorbar()
def plot_vel_redshift_evo(sim):
"""Plot the evolution with redshift of a simulation"""
halo = myname.get_name(sim, True)
vels = {}
for snap in (1, 3, 5):
hspec0 = ps.VWPlotSpectra(snap, halo)
(vbin, vels[snap]) = hspec0.vel_width_hist("Si", 2)
mm = np.min([np.size(vel) for vel in vels.values()])
#Normalised by z=3
plt.semilogx(vbin[:mm],
vels[5][:mm] / vels[3][:mm],
color="black",
ls="--")
plt.semilogx(vbin[:mm], vels[1][:mm] / vels[3][:mm], color="grey", ls="-")
plt.xlim(10, 1000)
plt.ylim(0.5, 1.5)
save_figure(path.join(outdir, "cosmo" + str(sim) + "_zz_evol"))
plt.clf()
def do_statistics(sim, snap):
"""Compute statistics"""
#Get Observational data
(_, met, vel) = vel_data.load_data(zrange[snap])
vel = np.log10(vel)
#Get Simulated data
halo = myname.get_name(sim, True)
hspec = ps.VWPlotSpectra(snap, halo)
svel = hspec.vel_width("Si", 2)
smet = hspec.get_metallicity()
#Ignore objects too faint to be seen
ind2 = np.where(smet > 1e-4)
smet = np.log10(smet[ind2])
svel = np.log10(svel[ind2])
#Fit to both datasets
(obs_intercept, obs_slope, obs_var) = ls.leastsq(vel, met)
(s_intercept, s_slope, s_var) = ls.leastsq(svel, smet)
print("obs fit: ", obs_intercept, obs_slope, np.sqrt(obs_var))
print("sim fit: ", s_intercept, s_slope, np.sqrt(s_var))
#Find correlations
print("obs pearson r: ", ls.pearson(vel, met, obs_intercept, obs_slope))
print("sim pearson r: ", ls.pearson(svel, smet, s_intercept, s_slope))
print("obs kstest: ", ls.kstest(vel, met, obs_intercept, obs_slope))
print("sim kstest: ", ls.kstest(svel, smet, s_intercept, s_slope))
#Now test whether they come from the same population
kss = hspec.kstest(10**met, 10**vel)
print("KS test between simulated and observed samples: ", kss)
#Do 200 trials and see how many times the KS test is worse
ntrials = 50
count = 0
for _ in range(ntrials):
rand = np.random.randint(0, np.size(svel), np.size(vel))
if kss <= hspec.kstest(10**smet[rand], 10**svel[rand]):
count += 1
print("Prob KS test between simulated samples was larger: ",
count * 1. / ntrials)
def test_noise():
"""Plot the effect of noise on the spectrum"""
halo = myname.get_name(7)
hspec = ps.VWPlotSpectra(3, halo, snr=0., label="No Noise")
hspec2 = ps.VWPlotSpectra(3, halo, snr=20., label="Noise")
plot_check(hspec, hspec2, "noise")
