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cleaned up analysis.py and plot.py in terms of comments.
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kpolsen committed Sep 11, 2017
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28 changes: 28 additions & 0 deletions Tables/Observations/SFR_Mstar/Jiang16.txt
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@@ -0,0 +1,28 @@
# ID age(M) mass(G) SFR_Lya SFR_UV E(B-V)
03 4 0.717 9.5 20.9 0.04
04 4 0.336 8.0 9.9 0.00
15 8 2.113 19.0 33.9 0.08
20 492 3.282 15.1 10.5 0.02
23 444 5.794 4.6 16.0 0.00
24 4 0.377 12.4 15.2 0.00
25 956 6.653 13.3 15.9 0.02
27 324 1.735 6.3 6.9 0.00
28 4 0.268 16.6 10.4 0.00
30 912 2.684 4.2 7.8 0.00
31 4 0.238 17.1 8.4 0.04
34 992 25.000 3.7 35.0 0.12
35 4 8.106 16.5 19.5 0.34
36 988 4.639 2.5 16.1 0.00
43 972 3.076 4.7 8.6 0.02
44 872 17.291 18.1 32.6 0.08
47 184 39.111 4.9 48.4 0.18
49 212 3.556 5.4 9.7 0.08
50 4 0.897 8.7 7.7 0.22
54 460 5.154 11.8 14.1 0.00
58 960 6.162 4.9 17.5 0.04
61 32 6.634 11.4 11.0 0.20
62 472 11.501 13.7 23.9 0.04
63 8 0.945 16.5 22.4 0.02
64 200 4.132 11.8 20.2 0.00
66 4 0.135 7.6 7.1 0.00
67 4 3.201 20.8 43.3 0.14
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57 changes: 30 additions & 27 deletions sigame/analysis.py
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Expand Up @@ -27,8 +27,19 @@
""" Global line luminosities """
#-------------------------------------------------------------------------------

def ISM_line_contributions(split=True,line='CII'):
print('Split L_[CII] into contributions from different ISM phases!')
def ISM_line_contributions(line='CII'):
'''
Purpose
---------
Splits line luminosity into contributions from different ISM phases
Arguments
---------
line: which line to plot - str
default = 'CII'
'''

print('')
plt.close('all') # close all windows

# Load model results
Expand Down Expand Up @@ -69,32 +80,18 @@ def ISM_line_contributions(split=True,line='CII'):

plt.savefig('plots/line_emission/ISM_contributions/['+line+']_lum_fractions_'+z1+ext_DENSE+ext_DIFFUSE+'.pdf', format='pdf') # .eps for paper!

print('Now plotting L_CII fractions vs mass fractions')

# Starting figure
fontsize = 13
mpl.rcParams['xtick.labelsize'] = fontsize
mpl.rcParams['ytick.labelsize'] = fontsize

xr = [0.1,100]
yr = [0.1,100]
# Set up figure
fig = plt.figure(1,figsize = (8,7))
ax1 = fig.add_subplot(1,1,1)
# xlog='y',ylog='y',\
# colored by ISM phase version
plot.simple_plot(add='y',xr=xr, yr=yr,\
xlab='Mass fraction [%]',ylab='Fraction of total L$_{[\mathrm{CII}]}$ [%]',\
x1=f_M[0],y1=f_L[0],ma1='x',fill1='y',ms1=6,mew1=2,col1='b',\
x2=f_M[1],y2=f_L[1],ma2='x',fill2='y',ms2=6,mew2=2,col2='orange',\
x3=f_M[2],y3=f_L[2],ma3='x',fill3='y',ms3=6,mew3=2,col3='r')

def ISM_line_efficiency(line='CII'):
'''
Purpose
---------
Plots the line efficiency (line luminosity / gas mass) in different ISM phases
plt.show(block=False)
plt.savefig('plots/line_emission/ISM_contributions/['+line+']_lum_mass_fractions_'+z1+ext_DENSE+ext_DIFFUSE+'.pdf', format='pdf') # .eps for paper!
Arguments
---------
line: which line to plot - str
default = 'CII'
'''

def ISM_line_efficiency(line='CII'):
print('Split L_[CII] into contributions from different ISM phases!')
plt.close('all') # close all windows

# Load model results
Expand Down Expand Up @@ -164,7 +161,13 @@ def ISM_line_efficiency(line='CII'):
#-------------------------------------------------------------------------------

def ISM_mass_contributions():
print('Investigate mass from different ISM phases!')
'''
Purpose
---------
Plots the mass contribution from different ISM phases
'''

plt.close('all') # close all windows

# Load model results
Expand Down
114 changes: 44 additions & 70 deletions sigame/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -859,7 +859,6 @@ def SFR_Mstar():
Plot of SFR vs stellar mass
'''

print('** Plot SFR vs stellar mass for sample **')
plt.close('all')

models = aux.find_model_results()
Expand All @@ -883,25 +882,18 @@ def SFR_Mstar():
age = 0.984 # age of universe, Omega_m = 0.3, Omega_lambda = 0.7, h = 0.65
MS = 10.**((0.84-0.026*age)*np.log10(xr)-(6.51-0.11*age))
# z ~ 6 LBGs and LAEs
# columns = ['No','M_1500','UV_slope','L_Lyalpha','ew_Lyalpha','SFR_UV','SFR_Lyalpha']
# J16 = pd.read_table('/Users/Karen/Desktop/temp/Observations/Jiang16_paper',names=columns,skiprows=5,sep=r'\t*',engine='python')
# columns = ['ID','age(M)','mass(G)','SFR_Lya','SFR_UV','E(B-V)']
# J16 = pd.read_table('sigame/temp/Observations/Jiang16.txt',names=columns,skiprows=1,sep=r'\s*',engine='python')
# SFR_J16 = J16['SFR_UV'].values
# No_J16 = J16['ID'].values
# ebv = J16['E(B-V)'].values
# age_J16 = J16['age(M)'].values
# M_star_J13 = np.array([7.2,3.4,21.1,32.8,57.9,3.8,66.5,17.4,2.7,26.8,2.4,250,81.1,46.4,30.8,172.9,391.1,35.6,9.0,51.5,61.6,66.3,115,9.4,41.3,1.4,32])*1e8
# No_J13 = np.array([3,4,15,20,23,24,25,27,28,30,31,34,35,36,43,44,47,49,50,54,58,61,62,63,64,66,67])
# SFR_J16 = [float(SFR_J16[No_J16 == No][0]) for No in No_J13]
# # From Linhua Jiang
# klambda = 8.5 #at 2200A
# SFR_J16 = SFR_J16 * 10.**(0.4*klambda*ebv)

if z1 == 'z2':
# eq. 28
age = 3.223 # age of universe [Gyr], Omega_m = 0.3, Omega_lambda = 0.7, h = 0.70
SFR_MS = 10.**((0.84-0.026*age)*np.log10(xr)-(6.51-0.11*age))
columns = ['ID','age(M)','mass(G)','SFR_Lya','SFR_UV','E(B-V)']
J16 = pd.read_table(d_t+'Observations/SFR_Mstar/Jiang16.txt',names=columns,skiprows=1,sep=r'\s*',engine='python')
SFR_J16 = J16['SFR_UV'].values
No_J16 = J16['ID'].values
ebv = J16['E(B-V)'].values
age_J16 = J16['age(M)'].values
M_star_J13 = np.array([7.2,3.4,21.1,32.8,57.9,3.8,66.5,17.4,2.7,26.8,2.4,250,81.1,46.4,30.8,172.9,391.1,35.6,9.0,51.5,61.6,66.3,115,9.4,41.3,1.4,32])*1e8
No_J13 = np.array([3,4,15,20,23,24,25,27,28,30,31,34,35,36,43,44,47,49,50,54,58,61,62,63,64,66,67])
SFR_J16 = [float(SFR_J16[No_J16 == No][0]) for No in No_J13]
# From Linhua Jiang
klambda = 8.5 #at 2200A
SFR_J16 = SFR_J16 * 10.**(0.4*klambda*ebv)

simple_plot(fignum=0,xlog='y',ylog='y',xr=xr,yr=yr,fontsize=16,\
xlab='M$_{\mathrm{*}}$ [M$_{\odot}$]',ylab='SFR [M$_{\odot}$ yr$^{-1}$]',legloc=[0.01,0.75],frameon=False,\
Expand All @@ -913,14 +905,14 @@ def SFR_Mstar():
x6=xr,y6=10.**(np.log10(MS)+3.*0.2),col6='k',lw6=1,ls6=':',legend=False)

ax1 = plt.gca()
# if z1 == 'z6':
# simple_plot(add='y',x1=M_star_J13[age_J16 > 30],y1=SFR_J16[age_J16 > 30],fill1='y',ma1='x',col1='r',ms1=10,mew1=2,lab1='Old $z\sim6$ LBGs/LAEs [Jiang+16]',\
# x2=M_star_J13[age_J16 < 30],y2=SFR_J16[age_J16 < 30],fill2='y',ma2='+',col2='b',ms2=11,mew2=2,lab2='Young $z\sim6$ LBGs/LAEs [Jiang+16]')
if z1 == 'z6':
simple_plot(add='y',x1=M_star_J13[age_J16 > 30],y1=SFR_J16[age_J16 > 30],fill1='y',ma1='x',col1='r',ms1=10,mew1=2,lab1='Old $z\sim6$ LBGs/LAEs [Jiang+16]',\
x2=M_star_J13[age_J16 < 30],y2=SFR_J16[age_J16 < 30],fill2='y',ma2='+',col2='b',ms2=11,mew2=2,lab2='Young $z\sim6$ LBGs/LAEs [Jiang+16]',legloc='upper left')

# Plot models
SC = ax1.scatter(M_star,SFR,marker='o',lw=2,s=64,c=ages,edgecolor='black',cmap='viridis',alpha=1,label='',zorder=10)
cbar = plt.colorbar(SC,pad=0)
cbar.set_label(label='Mass-weighted stellar age [Myr]')#,size=12) # colorbar in it's own axis
cbar.set_label(label='Mass-weighted stellar age [Myr]') # colorbar in it's own axis

plt.tight_layout()
plt.show(block=False)
Expand All @@ -942,35 +934,31 @@ def CII_SFR_z6(plot_models=True,plot_fits=True,plot_obs=True,twopanel=True,obs_g
models = aux.find_model_results()
for key in models.keys():
exec(key + '=models[key].values')
L_CII_tot = L_CII_GMC+L_CII_DNG+L_CII_DIG

z1 = 'z6'

# Plotting parameters
mpl.rcParams['xtick.minor.size'] = 4
mpl.rcParams['xtick.major.size'] = 6
mpl.rcParams['xtick.minor.width'] = 1.5
mpl.rcParams['xtick.major.width'] = 1.5
fs_labels = 20
if twopanel: fs_labels = 17

# Plot parameters, quickly change y or x range here
# Change y or x range here
xr = 10.**np.array([0,3.05]) # SFR range
yr = 10.**np.array([6.5,9.8]) # [CII] range
if not twopanel: fig = plt.figure(figsize = (12,9))
if twopanel: fig = plt.figure(figsize = (18,8))

# Load [CII] luminosities
sims = cl.sim(sim_paths)
L_CII_tot = L_CII_GMC+L_CII_DNG+L_CII_DIG

if not twopanel:
ax1 = fig.add_subplot(1,1,1)
if twopanel:
fig = plt.figure(figsize = (18,8))
gs = gridspec.GridSpec(1, 2, width_ratios=[6, 5])
ax1 = plt.subplot(gs[1])
if not twopanel:
fig = plt.figure(figsize = (12,9))
ax1 = fig.add_subplot(1,1,1)
ax1.set_xlabel('SFR [M$_{\odot}$ yr$^{-1}$]',fontsize=fs_labels)
ax1.set_ylabel('L$_{[\mathrm{CII}]}$ [L$_{\odot}$]',fontsize=fs_labels)
ax1.set_xlim(xr)
ax1.set_ylim(yr)
ax1.set_xlabel('SFR [M$_{\odot}$ yr$^{-1}$]',fontsize=fs_labels)
xlab = ax1.get_xticks()
ylab = ax1.get_yticks()
ax1.set_xticklabels(xlab,fontsize=fs_labels)
Expand All @@ -984,46 +972,37 @@ def CII_SFR_z6(plot_models=True,plot_fits=True,plot_obs=True,twopanel=True,obs_g
# Models!
# ======================================================================

# Powerlaw fit to high-z observations [de Looze et al. 2014]
# logL_CII = np.array([4,11])
# logSFR = -8.52+1.18*logL_CII
# fit0 = ax1.plot(10.**logSFR,10.**logL_CII,c='purple',ls='--',lw=lw)
# Powerlaw fit to z=0 metal-poor dwarf galaxies
# Powerlaw fit to z=0 metal-poor dwarf galaxies [de Looze et al. 2014]
logL_CII = np.array([4,11])
logSFR = -5.73+0.80*logL_CII
ax1.fill_between(10.**logSFR, 10.**(logL_CII-0.37), 10.**(logL_CII+0.37), facecolor='lightgrey', linewidth=0, alpha=0.5)
fit0 = ax1.plot(10.**logSFR,10.**logL_CII,c='grey',ls='--',lw=lw)
# Powerlaw fit to z=0 starburst galaxies
# Powerlaw fit to z=0 starburst galaxies [de Looze et al. 2014]
logL_CII = np.array([4,11])
logSFR = -7.06+1.00*logL_CII
ax1.fill_between(10.**logSFR, 10.**(logL_CII-0.27), 10.**(logL_CII+0.27), facecolor='lightgrey', linewidth=0, alpha=0.5)
fit1 = ax1.plot(10.**logSFR,10.**logL_CII,c='grey',ls='--',dashes=(1,4),lw=lw)
print('\nAverage factor below de Looze+14 metal-poor dwarfs')

# Powerlaw fit to z=0 observations [Malhotra et al. 2001]
# L_FIR = xr*3.4e9
# L_CII = 10.**(-2.51+np.log10(L_FIR))
# fit1 = ax1.plot(xr,L_CII,'--',dashes=(2,5),c='teal',lw=lw)

# Powerlaw fit to model galaxies at z=6
slope_models,intercept_models,slope_dev,inter_dev = aux.lin_reg_boot(np.log10(SFR),np.log10(L_CII_tot))

# Making different line styles for the SFR-range covered by the simulations and
# the SFR-range where an extrapolation is necessary
L_CII_model = 10.**(slope_models*np.log10(xr)+intercept_models)
xr2 = [min(SFR),max(SFR)]
L_CII_model2 = 10.**(slope_models*np.log10(xr2)+intercept_models)
# dex spread around relation:
dex = np.std(np.abs(np.log10(L_CII_tot)-(slope_models*np.log10(SFR)+intercept_models)))
print('Dex: %s' % dex)

if not twopanel:
if plot_models:
fit = ax1.plot(xr,L_CII_model,ls='--',color='purple',lw=1.8)
fit = ax1.plot(xr2,L_CII_model2,ls='-',color='purple',lw=1.8)
fit = ax1.plot(xr,L_CII_model,ls='--',color='purple',lw=1.8)
fit = ax1.plot(xr2,L_CII_model2,ls='-',color='purple',lw=1.8)

if plot_fits:
# Powerlaw fit to Vallini+15, z~7 eq. 8
sims = cl.sim(sim_paths)
Zfit = np.mean(sims.Zmw())
L_CII_V15 = 10.**(7.0 + 1.2*np.log10(xr) + 0.021*np.log10(Zfit) + \
0.012*np.log10(xr)*np.log10(Zfit) - 0.74*np.log10(Zfit)**2.)
Expand All @@ -1033,7 +1012,7 @@ def CII_SFR_z6(plot_models=True,plot_fits=True,plot_obs=True,twopanel=True,obs_g

# PCA fit to L_[CII](SFR,Z)
Zfit2 = np.mean(Zsfr)
L_CII_PCA = 10.**(7.26+0.35*np.log10(xr)+0.38*np.log10(Zfit2))
L_CII_PCA = 10.**(7.17+0.55*np.log10(xr)+0.23*np.log10(Zfit2))
ax1.plot(xr,L_CII_PCA,c='purple',ls='--',dashes=(6,4,1,4,1,4),lw=lw)

if len(galnames) > 1:
Expand All @@ -1050,19 +1029,20 @@ def CII_SFR_z6(plot_models=True,plot_fits=True,plot_obs=True,twopanel=True,obs_g
rms_dex = np.sqrt(np.sum(dev**2./len(dev)))
print('rms error of: '+str(rms_dex)+' dex')

print('On average this far below observed relation:')
L_CII_obs = 10.**((np.log10(SFR)+7.06)/1.00)
print(str(np.mean((L_CII_obs-L_CII_tot)/L_CII_obs)*100.)+' %')
print(str(np.mean(np.log10(L_CII_obs)-np.log10(L_CII_tot)))+' dex')
print('Power law fit this far above Vallini+15:')
L_CII_V15 = 10.**(7.0 + 1.2*np.log10(min(SFR)) + 0.021*np.log10(Zfit) + \
0.012*np.log10(min(SFR))*np.log10(Zfit) - 0.74*np.log10(Zfit)**2.)
L_CII = 10.**(slope_models*np.log10(min(SFR))+intercept_models)
print('at min SFR : '+str(np.log10(L_CII)-np.log10(L_CII_V15))+' dex')
L_CII_V15 = 10.**(7.0 + 1.2*np.log10(max(SFR)) + 0.021*np.log10(Zfit) + \
0.012*np.log10(max(SFR))*np.log10(Zfit) - 0.74*np.log10(Zfit)**2.)
L_CII = 10.**(slope_models*np.log10(max(SFR))+intercept_models)
print('at max SFR : '+str(np.log10(L_CII)-np.log10(L_CII_V15))+' dex')
if len(galnames) > 1:
print('On average this far below observed relation:')
L_CII_obs = 10.**((np.log10(SFR)+7.06)/1.00)
print(str(np.mean((L_CII_obs-L_CII_tot)/L_CII_obs)*100.)+' %')
print(str(np.mean(np.log10(L_CII_obs)-np.log10(L_CII_tot)))+' dex')
print('Power law fit this far above Vallini+15:')
L_CII_V15 = 10.**(7.0 + 1.2*np.log10(min(SFR)) + 0.021*np.log10(Zfit) + \
0.012*np.log10(min(SFR))*np.log10(Zfit) - 0.74*np.log10(Zfit)**2.)
L_CII = 10.**(slope_models*np.log10(min(SFR))+intercept_models)
print('at min SFR : '+str(np.log10(L_CII)-np.log10(L_CII_V15))+' dex')
L_CII_V15 = 10.**(7.0 + 1.2*np.log10(max(SFR)) + 0.021*np.log10(Zfit) + \
0.012*np.log10(max(SFR))*np.log10(Zfit) - 0.74*np.log10(Zfit)**2.)
L_CII = 10.**(slope_models*np.log10(max(SFR))+intercept_models)
print('at max SFR : '+str(np.log10(L_CII)-np.log10(L_CII_V15))+' dex')

# Powerlaw fit to model galaxies at z=2 [Olsen+15]
L_CII_model_z2 = 0.78e7*xr**1.27
Expand Down Expand Up @@ -1113,11 +1093,9 @@ def CII_SFR_z6(plot_models=True,plot_fits=True,plot_obs=True,twopanel=True,obs_g
ax1.fill_between(10.**logSFR, 10.**(logL_CII-0.27), 10.**(logL_CII+0.27), facecolor='lightgrey', linewidth=0, alpha=0.5,zorder=0)
fit1 = ax1.plot(10.**logSFR,10.**logL_CII,c='grey',ls='--',dashes=(1,4),lw=lw,zorder=0)

# pdb.set_trace()
if plot_obs: add_observations_to_plot(slope_models,intercept_models,mark_reasons,mark_uplim,mark_det,z1=z1)

# Legends for observations!
# get handles
if plot_models: ax1.scatter([1e20,1e30],[1e20,1e30],marker='o',s=64,color='lightseagreen',label=r'S$\mathrm{\'I}$GAME (this work)$_{}$',lw=2,edgecolor='black')
handles2, labels2 = ax1.get_legend_handles_labels()
# remove the errorbars
Expand All @@ -1130,14 +1108,12 @@ def CII_SFR_z6(plot_models=True,plot_fits=True,plot_obs=True,twopanel=True,obs_g
ax1.legend(handles2, labels2, loc='upper left',fontsize=11,frameon=False,numpoints=1,borderpad=1)

# Model galaxies
# L_CII_tot = L_CII_tot*0.+10.**6.6
ax1.xaxis.set_major_formatter(ScalarFormatter())
if plot_models:
plot = ax1.scatter(SFR,L_CII_tot,marker='o',edgecolor='black',c=np.log10(SFRsd),s=64,lw=2,cmap='viridis',zorder=200)
cbar = fig.colorbar(plot,ax=ax1,pad=0)#,cax = cbar_ax)
cbar.set_label(label=getlabel('lSFRsd'),size=13)#,weight='bold')


for axis in ['top','bottom','left','right']:
ax1.spines[axis].set_linewidth(1.)

Expand Down Expand Up @@ -1599,10 +1575,8 @@ def grid_parameters(histo_color='teal',FUV=5,ISM_phase='GMC',figsize=(10,7)):
if histo_color == 'colsel': ax1.legend(loc='upper left')

panel += 1
# plt.suptitle('Grid points (dashed lines) on histograms (solid lines) in diffuse gas')
plt.show(block=False)
plt.savefig('plots/diffuse_gas/grid_parameters/difgrid_points_on_histos'+ext_DIFFUSE+'_'+z1+'.pdf',format='pdf') # .eps for paper!
# fig.savefig('plots/dif/grids/grid_points_on_histos_paper.png', dpi=fig.dpi)

#===============================================================================
""" Gas distribution plots """
Expand Down

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