def test_load_sngl():
# Class
cos_halos = COSHalos(fits_path=data_path(''),
cdir=data_path(''),
load=False)
# Load
cos_halos.load_single_fits(('J0950+4831', '177_27'))
def test_getitem():
# Class
cos_halos = COSHalos(fits_path=data_path(''), cdir='dum', load=False)
# Load
cos_halos.load_single_fits(('J0950+4831', '177_27'))
# Get item
cgm_abs = cos_halos[('J0950+4831', '177_27')]
assert cgm_abs.galaxy.field == 'J0950+4831'
def fig_lya(inp=('J1555+3628', '88_11'), outfil='fig_j1555_lya.png'):
# Init COS-Halos sightline
cos_halos = COSHalos()
#cos_halos.load_single( ('J0950+4831','177_27'))
cgm_abs = cos_halos[inp]
# ########################################
# Finder (out of order to avoid PDF issues)
#finder.main([cgm_abs.name, cgm_abs.galaxy.coord], imsize=2.*u.arcmin, show_circ=False)
lclr = 'blue'
lw = 2.
# Start the plot
#outfil='fig_j1555_lya.pdf'
#pp = PdfPages(outfil)
# Full QSO spectrum
spec = cos_halos.load_bg_cos_spec(inp, 1215.6700 * u.AA)
plt.figure(figsize=(5, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
# Axes
ax = plt.subplot(gs[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(1436., 1455.)
ax.set_ylim(-0.1, 1.3)
ax.set_ylabel('Normalized Flux')
ax.set_xlabel(r'Wavelength ($\AA$)')
for axis in ['top', 'bottom', 'left', 'right']:
ax.spines[axis].set_linewidth(2.0)
# Zero line
ax.plot([-1e9, 1e9], (0., 0.), 'g--', lw=lw)
wv_lya = 1215.670 * (1 + cgm_abs.zabs)
ax.plot([wv_lya] * 2, [-1e9, 1e9], 'b--', lw=lw)
# Data
ax.plot(spec.wavelength, spec.flux, 'k', drawstyle='steps-mid')
ax.plot(spec.wavelength, spec.sig, 'r:')
#ax.fill_between( [1455., 1490.], [ymnx[0]]*2, [ymnx[1]]*2, color='blue', alpha=0.3)
# Label
ax.text(1437., 0.3, r'HI Ly$\alpha$', 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)
plt.savefig(outfil)
plt.close()
print("Wrote {:s}".format(outfil))
def test_load_survey():
# Class
cos_halos = COSHalos() #debug=True)
assert len(cos_halos.cgm_abs) == 44
# Metallicity
cos_halos.load_mtl_pdfs()
# Confirm J0943+0531_227_19 is out for metallicity
cgm_j0943 = cos_halos[('J0943+0531', '227_19')]
assert cgm_j0943.igm_sys.metallicity is None
def test_write_sngl():
import io, json
from linetools import utils as ltu
# Class
cos_halos = COSHalos(fits_path=data_path(''),
cdir=data_path(''),
load=False)
# Load
cos_halos.load_single_fits(('J0950+4831', '177_27'))
# Write to JSON
cdict = cos_halos.cgm_abs[0].to_dict()
ltu.savejson('tmp.json', cdict, overwrite=True)
def test_PDF():
cos_halos = COSHalos()
cos_halos.load_mtl_pdfs()
all_NHI = []
all_mtl = []
for sl, sightline in enumerate(cos_halos.cgm_abs):
if sightline.igm_sys.NHIPDF is not None:
this_nhi = sightline.igm_sys.NHIPDF.median
all_NHI.append(this_nhi)
all_mtl.append(sightline.igm_sys.metallicity.median)
# Test
assert len(all_NHI) == 31
def fig_experiment(outfil=None):
# Init COS-Halos sightline
cos_halos = COSHalos()
cos_halos.load_single(('J0950+4831', '177_27'))
cgm_abs = cos_halos.cgm_abs[0]
print('zem = {:g}'.format(cgm_abs.abs_sys.zem))
# ########################################
# Finder (out of order to avoid PDF issues)
#finder.main([cgm_abs.name, cgm_abs.galaxy.coord], imsize=2.*u.arcmin, show_circ=False)
lclr = 'blue'
# Start the plot
if outfil is None:
outfil = 'fig_experiment.pdf'
pp = PdfPages(outfil)
# Full QSO spectrum
spec_fil = os.getenv(
'DROPBOX_DIR'
) + '/COS-Halos/Targets/J0950+4831/Data/J0950+4831_nbin6_coadd.fits'
spec = lsio.readspec(spec_fil)
xmnx = (1135., 1750.)
ymnx = (-0.0002, 0.0106)
for ss in range(2):
plt.figure(figsize=(8, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
# Axes
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(1135., 1750.)
ax.set_ylim(-0.0002, 0.0106)
ax.set_ylabel('Relative Flux')
ax.set_xlabel(r'Wavelength ($\AA$)')
# Zero line
ax.plot(xmnx, (0., 0.), 'g--')
# Data
ax.plot(spec.dispersion, spec.flux, 'k')
ax.plot(spec.dispersion, spec.sig, 'r:')
if ss > 0:
ax.fill_between([1455., 1490.], [ymnx[0]] * 2, [ymnx[1]] * 2,
color='blue',
alpha=0.3)
# Label
ax.text(1500.,
0.008,
cgm_abs.field,
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()
# Lya spec
for ss in range(3):
plt.figure(figsize=(8, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
# Axes
if ss == 0:
spec = cos_halos.load_bg_cos_spec(0, 1215.6700 * u.AA)
wvmnx = np.array([1455., 1490.]) * u.AA
scl_wv = 1.
elif ss == 1:
scl_wv = (1 + cgm_abs.galaxy.z)
elif ss == 2:
spec = cos_halos.load_bg_cos_spec(0, 1025.7222 * u.AA)
scl_wv = (1 + cgm_abs.galaxy.z)
wvmnx = np.array([1015., 1037.]) * u.AA * scl_wv # convoluted, yes
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(wvmnx.value / scl_wv)
ax.set_ylim(-0.1, 1.3)
ax.set_ylabel('Normalized Flux')
# Zero line
ax.plot(wvmnx.value / scl_wv, (0., 0.), 'g--')
# Data
ax.plot(spec.dispersion / scl_wv, spec.flux, 'k')
ax.plot(spec.dispersion / scl_wv, spec.sig, 'r:')
# Label
if ss == 0:
ax.set_xlabel(r'Wavelength ($\AA$)')
ax.text(1480.,
0.4,
cgm_abs.field,
ha='left',
fontsize=21.,
color=lclr)
elif ss == 1:
ax.set_xlabel(r'Rest Wavelength ($\AA$)')
ax.text(1220.,
0.4,
r'HI Ly$\alpha$' + ' \n ' +
r'$z=${:0.4f}'.format(cgm_abs.galaxy.z),
ha='left',
fontsize=21.,
multialignment='center',
color=lclr)
elif ss == 2:
ax.set_xlabel(r'Rest Wavelength ($\AA$)')
ax.text(1017.,
0.4,
r'HI Ly$\beta$' + ' \n ' +
r'$z=${:0.4f}'.format(cgm_abs.galaxy.z),
ha='left',
fontsize=21.,
multialignment='center',
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()
# ########################################
# Galaxy spectrum
plt.figure(figsize=(8, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
# Load
spec = cos_halos.load_gal_spec(0)
# Axes
ax = plt.subplot(gs[0, 0])
ax.set_xlim(4000., 8000.)
ax.set_ylim(-0.1, 25.)
ax.set_xlabel(r'Wavelength ($\AA$)')
ax.set_ylabel('Relative Flux')
# Velo
ax.plot(spec.dispersion, spec.flux, 'k') #, lw=1.3)
ax.plot(spec.dispersion, spec.sig, 'r:') #, lw=1.3)
# Label
#ax.text(-800., 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()
# ########################################
# Simple HI stack plot
trans = np.array([1215.6701, 1025.7223]) * u.AA
lbls = [r'HI Ly$\alpha$', r'HI Ly$\beta$']
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(-1000., 1000.)
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, 'k', drawstyle='steps', lw=1.3)
# Label
ax.text(-800., 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()
# ########################################
# Greater stack plot
trans = np.array([
1215.6701, 1025.7223, 2852.9642, 2803.5315, 1083.9937, 1206.5,
1393.755, 1037.6167
]) * u.AA
lbls = [
r'HI Ly$\alpha$', r'HI Ly$\beta$', 'MgI 2852', 'MgII 2796', 'NII 1083',
'SiIII 1206', 'SiIV 1393', 'OVI 1037'
]
plt.figure(figsize=(8, 5))
plt.clf()
gs = gridspec.GridSpec(2, 4)
xmnx = (-500., 500.)
ymnx = (-0.1, 1.3)
wbox = {'facecolor': 'white', 'edgecolor': 'white'}
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 % 2, qq // 2])
ax.set_xlim(xmnx)
ax.xaxis.set_major_locator(plt.MultipleLocator(300.))
ax.set_ylim(ymnx)
if qq % 2 == 0:
ax.xaxis.set_ticklabels([])
if qq < 2:
ax.set_ylabel('Normalized Flux')
else:
ax.yaxis.set_ticklabels([])
#if qq == 3:
# ax.set_xlabel('Relative Velocity (km/s)')
# Velo
velo = spec.relative_vel(itran * (cgm_abs.galaxy.z + 1))
ax.plot(velo, spec.flux, 'k', drawstyle='steps', lw=1.3)
ax.plot([0., 0.], ymnx, 'g:')
# Label
ax.text(10., 1.15, lbl, ha='left', fontsize=15., color=lclr, bbox=wbox)
# 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_abs_gallery(wrest=None,
lbl=None,
outfil=None,
cos_halos=None,
passback=False,
axes_flg=0):
# import tlk_coshalos as tch
# reload(tch)
# cos_halos = tch.fig_abs_gallery(passback=True)
'''Gallery of absorption lines
Default is M* vs. sSFR
But you can do rho vs. M* too
axes_flg: int, optional
0: M* vs. sSFR
1: rho vs. M*
'''
# Linelist
llist = lll.LineList('Strong')
if wrest is None:
wrest = 1215.670 * u.AA
Zion = (llist[wrest]['Z'], llist[wrest]['ion'])
if lbl is None:
lbl = r'HI Ly$\alpha$'
if outfil is None:
outfil = 'fig_HI_gallery.pdf'
# Init COS-Halos (slow)
if cos_halos is None:
cos_halos = COSHalos()
cos_halos.load_mega() #skip_ions=True)
if passback:
return cos_halos
if axes_flg == 0:
xmnx = (9.4, 11.7)
ymnx = (-13., -9.)
elif axes_flg == 1:
ymnx = (9.4, 11.7) # log Msun
xmnx = (15., 163) # kpc
vmnx = (-600., 600.) # km/s
wbox = {'facecolor': 'white', 'edgecolor': 'white'}
lclr = 'blue'
# To help with looping
def sngl_abs(ax,
field_gal,
wbox=wbox,
lclr=lclr,
vmnx=vmnx,
xmnx=xmnx,
ymnx=ymnx,
cos_halos=cos_halos,
show_xylbl=True,
srect=0.2,
show_ewlbl=True,
lw=1.3,
axes_flg=axes_flg):
#
cgm_abs = cos_halos[field_gal]
if axes_flg == 0:
xplt = cgm_abs.galaxy.stellar_mass
yplt = np.log10(
cgm_abs.galaxy.sfr[1]) - cgm_abs.galaxy.stellar_mass
elif axes_flg == 1:
yplt = cgm_abs.galaxy.stellar_mass
xplt = cgm_abs.rho.value
# Spec
spec = cos_halos.load_bg_cos_spec(field_gal, wrest)
velo = spec.relative_vel(wrest * (cgm_abs.galaxy.z + 1))
# EW
data = cgm_abs.abs_sys.ions[Zion]
itrans = np.where(np.abs(data['LAMBDA'] - wrest.value) < 1e-3)[0]
if len(itrans) == 0:
print('No measurement of {:g} for {:s} {:s}'.format(
wrest, field_gal[0], field_gal[1]))
return
EW = data['WREST'][itrans][0] * u.AA / 1e3
sigEW = data['SIGWREST'][itrans][0] * u.AA / 1e3
if sigEW <= 0.: # Something must be wrong
return
if EW > 3 * sigEW:
sclr = 'k'
else:
sclr = 'r'
#
xrect = (xplt - xmnx[0]) / (xmnx[1] - xmnx[0])
yrect = (yplt - ymnx[0]) / (ymnx[1] - ymnx[0])
rect = [xrect, yrect, srect, srect]
axsp = xpsimp.add_subplot_axes(ax, rect) #,axisbg=axisbg)
axsp.set_xlim(vmnx)
axsp.set_ylim(-0.1, 1.3)
if show_xylbl:
axsp.set_xlabel('Relative Velocity (km/s)', fontsize=9.)
axsp.set_ylabel('Normalized Flux', fontsize=9.)
# Plot
axsp.plot(velo, spec.flux, sclr, drawstyle='steps', lw=lw)
# Label
#llbl = (r'$W_\lambda = $'+'{:0.2f} A \n'.format(EW.value)+
# '$z=${:.3f}\n'.format(cgm_abs.galaxy.z)+
# r'$\rho=$'+'{:d}kpc'.format(int(np.round(cgm_abs.rho.to('kpc').value))))
if show_ewlbl:
llbl = r'$W_\lambda = $' + '{:0.2f} A'.format(EW.value)
axsp.text(-300.,
1.1,
llbl,
ha='left',
fontsize=7.,
color=lclr,
bbox=wbox) #multialignment='left')
# Start the plot
pp = PdfPages(outfil)
if axes_flg == 0:
loop = range(4)
else:
loop = range(3, 4)
for ss in loop:
plt.figure(figsize=(8, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
# Axes
ax = plt.subplot(gs[0, 0])
ax.set_xlim(xmnx)
ax.set_ylim(ymnx)
if axes_flg == 0:
ax.set_ylabel('sSFR')
ax.set_xlabel('log M*')
ax.text(9.75, -12., lbl, color=lclr, fontsize=21.)
elif axes_flg == 1:
ax.set_ylabel('log M*')
ax.set_xlabel('Impact Parameter (kpc)')
ax.text(40., 11.5, lbl, color=lclr, fontsize=21.)
#ax.xaxis.set_major_locator(plt.MultipleLocator(300.))
#
if ss == 0: # Single system
field_gal = ('J0950+4831', '177_27')
sngl_abs(ax, field_gal)
elif ss == 1: # Two systems
cgm_list = [('J0950+4831', '177_27'), ('J1245+3356', '236_36')]
for field_gal in cgm_list:
sngl_abs(ax, field_gal)
elif ss > 1: # Half systems
if ss == 2:
iend = 20
else:
iend = -1
for cgm_abs in cos_halos.cgm_abs[0:iend]:
field_gal = (cgm_abs.field, cgm_abs.gal_id)
sngl_abs(ax,
field_gal,
show_xylbl=False,
srect=0.1,
show_ewlbl=False,
lw=0.5)
else:
pass
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_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_sngl_metPDF(system):
""" Shows a single metallicity PDF
"""
from matplotlib import transforms
# Read Metallicity input
mfile = '../Analysis/COS_Halos_MTL.ascii'
data = Table.read(mfile, format='ascii')
mtl_inps = np.where(data['name'] == system[0]+'_'+system[1])[0]
ion_lst = []
clrs = []
cdict = {0:'black', -1:'red', -2:'green'}
for inp in mtl_inps:
ion_lst.append(data[inp]['ion'])
clrs.append(cdict[data[inp]['flag']])
# Read COS-Halos
cos_halos = COSHalos()
cos_halos.load_single_fits(system, skip_ions=True)
orig_NHI = cos_halos.NHI
orig_fNHI = cos_halos.flag_NHI
# Read PDF
mtlfil = '../Analysis/COS_Halos_MTL.hdf5'
fh5 = h5py.File(mtlfil,'r')
mPDF = MetallicityPDF(fh5['met']['left_edge_bins']+
fh5['met']['left_edge_bins'].attrs['BINSIZE']/2.,
fh5['met'][system[0]+'_'+system[1]])
# KLUDGE
print("BIG KLUDGE HERE")
bad = np.where(mPDF.ZH < -2)[0]
mPDF.pdf_ZH[bad] = 0.
mPDF.normalize()
# Init
NHI_mnx = (14.8, 19.1)
# Start the plot
outfil = 'fig_metPDF_'+system[0]+'_'+system[1]+'.pdf'
pp = PdfPages(outfil)
fig = plt.figure(figsize=(7, 4))
plt.clf()
ax = plt.gca()
# Axes
#wvmnx = awvmnx[iuvq['instr']]
#ax.xaxis.set_minor_locator(plt.MultipleLocator(500.))
#ax.yaxis.set_major_locator(plt.MultipleLocator(1.))
#plt.ylim(0, nsys+1)
ax.set_xlim(-2,1)
# Labels
lsz = 19.
# Giddy up
ax.bar(mPDF.ZH-mPDF.dZH/2., mPDF.pdf_ZH, width=mPDF.dZH)
ax.set_xlabel("[Z/H]", size=lsz)
ax.set_ylabel("PDF", size=lsz)
# Label system
csz = 18.
lbl = '{:s}_{:s}'.format(system[0], system[1])
ax.text(0.1, 0.87, lbl, transform=ax.transAxes, color='black',
size=csz, ha='left')
# Ions
x = -1.8
ymnx = ax.get_ylim()
y = 0.75 * ymnx[1]
isz = 14.
t = plt.gca().transData
for s,c in zip(ion_lst,clrs):
text = plt.text(x,y," "+s+" ",color=c, transform=t, size=isz)
text.draw(fig.canvas.get_renderer())
ex = text.get_window_extent()
t = transforms.offset_copy(text._transform, x=ex.width*0.9, units='dots')
# End
xputils.set_fontsize(ax, 16.)
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
def fig_diff_NHI(cos_halos=None, outfil='fig_diff_NHI.pdf'):
""" Compares original NHI with new
"""
# Read LLS
jfile = '../Analysis/COS_Halos_LLS.json'
with open(jfile) as json_file:
fdict = json.load(json_file)
# Read COS-Halos
if cos_halos is None:
cos_halos = COSHalos()
cos_halos.load_mega(skip_ions=True)
orig_NHI = cos_halos.NHI
orig_fNHI = cos_halos.flag_NHI
# Init
NHI_mnx = (14., 21.)
# Start the plot
if outfil is not None:
pp = PdfPages(outfil)
plt.figure(figsize=(5, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
ax = plt.subplot(gs[0])
# Axes
#wvmnx = awvmnx[iuvq['instr']]
#ax.xaxis.set_minor_locator(plt.MultipleLocator(500.))
#ax.yaxis.set_major_locator(plt.MultipleLocator(1.))
ax.minorticks_on()
ax.set_xlim(NHI_mnx)
ax.set_ylim(NHI_mnx)
# Labels
ax.set_xlabel(r'Original: $\log_{10} \, N_{\rm HI}$')
ax.set_ylabel(r'New: $\log_{10} \, N_{\rm HI}$')
# Loop on Systems
for key in fdict.keys():
# Original
mt = np.where((cos_halos.field==fdict[key]['quasar']) &
(cos_halos.gal_id==fdict[key]['galaxy']))[0]
if len(mt) != 1:
raise ValueError("Not a proper match")
# Plot
if orig_fNHI[mt] == 1:
warnings.warn("Assuming the value for {:s}_{:s} is a lower limit".format(
fdict[key]['quasar'],fdict[key]['galaxy']))
#ax.quiver(orig_NHI[mt], fdict[key]['fit_NHI'][0], 1, 0,
# units='x', width=0.03, headwidth=2., headlength=5.)
elif orig_fNHI[mt] == 2:
pass
#ax.quiver(orig_NHI[mt], fdict[key]['fit_NHI'][0], 1, 0,
# units='x', width=0.03, headwidth=2., headlength=5.)
elif orig_fNHI[mt] == 3:
raise ValueError("Very Unlikely")
else:
raise ValueError("Nope")
# New
#xdb.set_trace()
yerr=[[fdict[key]['fit_NHI'][0]-fdict[key]['fit_NHI'][1]],
[fdict[key]['fit_NHI'][2]-fdict[key]['fit_NHI'][0]]]
ax.errorbar([orig_NHI[mt]], [fdict[key]['fit_NHI'][0]], yerr=yerr,
capthick=2, fmt='o')
# 1-1 line
ax.plot(NHI_mnx, NHI_mnx, ':', color='gray')
# End
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
def test_data_for_survey():
cos_halos = COSHalos()
assert isinstance(cos_halos._data, Table)
# Add an ion
cos_halos.add_ion_to_data('OVI')
assert 'flag_N_OVI' in cos_halos._data.keys()
def test_write_to_json():
cos_halos = COSHalos()
cos_halos.to_json(data_path('cos_halos.json'))
def fig_sngl_metPDF(system):
""" Shows a single metallicity PDF
"""
from matplotlib import transforms
# Read Metallicity input
mfile = '../Analysis/COS_Halos_MTL.ascii'
data = Table.read(mfile, format='ascii')
mtl_inps = np.where(data['name'] == system[0] + '_' + system[1])[0]
ion_lst = []
clrs = []
cdict = {0: 'black', -1: 'red', -2: 'green'}
for inp in mtl_inps:
ion_lst.append(data[inp]['ion'])
clrs.append(cdict[data[inp]['flag']])
# Read COS-Halos
cos_halos = COSHalos()
cos_halos.load_single_fits(system, skip_ions=True)
orig_NHI = cos_halos.NHI
orig_fNHI = cos_halos.flag_NHI
# Read PDF
mtlfil = '../Analysis/COS_Halos_MTL.hdf5'
fh5 = h5py.File(mtlfil, 'r')
mPDF = MetallicityPDF(
fh5['met']['left_edge_bins'] +
fh5['met']['left_edge_bins'].attrs['BINSIZE'] / 2.,
fh5['met'][system[0] + '_' + system[1]])
# KLUDGE
print("BIG KLUDGE HERE")
bad = np.where(mPDF.ZH < -2)[0]
mPDF.pdf_ZH[bad] = 0.
mPDF.normalize()
# Init
NHI_mnx = (14.8, 19.1)
# Start the plot
outfil = 'fig_metPDF_' + system[0] + '_' + system[1] + '.pdf'
pp = PdfPages(outfil)
fig = plt.figure(figsize=(7, 4))
plt.clf()
ax = plt.gca()
# Axes
#wvmnx = awvmnx[iuvq['instr']]
#ax.xaxis.set_minor_locator(plt.MultipleLocator(500.))
#ax.yaxis.set_major_locator(plt.MultipleLocator(1.))
#plt.ylim(0, nsys+1)
ax.set_xlim(-2, 1)
# Labels
lsz = 19.
# Giddy up
ax.bar(mPDF.ZH - mPDF.dZH / 2., mPDF.pdf_ZH, width=mPDF.dZH)
ax.set_xlabel("[Z/H]", size=lsz)
ax.set_ylabel("PDF", size=lsz)
# Label system
csz = 18.
lbl = '{:s}_{:s}'.format(system[0], system[1])
ax.text(0.1,
0.87,
lbl,
transform=ax.transAxes,
color='black',
size=csz,
ha='left')
# Ions
x = -1.8
ymnx = ax.get_ylim()
y = 0.75 * ymnx[1]
isz = 14.
t = plt.gca().transData
for s, c in zip(ion_lst, clrs):
text = plt.text(x, y, " " + s + " ", color=c, transform=t, size=isz)
text.draw(fig.canvas.get_renderer())
ex = text.get_window_extent()
t = transforms.offset_copy(text._transform,
x=ex.width * 0.9,
units='dots')
# End
xputils.set_fontsize(ax, 16.)
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
def fig_diff_NHI(cos_halos=None, outfil='fig_diff_NHI.pdf'):
""" Compares original NHI with new
"""
# Read LLS
jfile = '../Analysis/COS_Halos_LLS.json'
with open(jfile) as json_file:
fdict = json.load(json_file)
# Read COS-Halos
if cos_halos is None:
cos_halos = COSHalos()
cos_halos.load_mega(skip_ions=True)
orig_NHI = cos_halos.NHI
orig_fNHI = cos_halos.flag_NHI
# Init
NHI_mnx = (14., 21.)
# Start the plot
if outfil is not None:
pp = PdfPages(outfil)
plt.figure(figsize=(5, 5))
plt.clf()
gs = gridspec.GridSpec(1, 1)
ax = plt.subplot(gs[0])
# Axes
#wvmnx = awvmnx[iuvq['instr']]
#ax.xaxis.set_minor_locator(plt.MultipleLocator(500.))
#ax.yaxis.set_major_locator(plt.MultipleLocator(1.))
ax.minorticks_on()
ax.set_xlim(NHI_mnx)
ax.set_ylim(NHI_mnx)
# Labels
ax.set_xlabel(r'Original: $\log_{10} \, N_{\rm HI}$')
ax.set_ylabel(r'New: $\log_{10} \, N_{\rm HI}$')
# Loop on Systems
for key in fdict.keys():
# Original
mt = np.where((cos_halos.field == fdict[key]['quasar'])
& (cos_halos.gal_id == fdict[key]['galaxy']))[0]
if len(mt) != 1:
raise ValueError("Not a proper match")
# Plot
if orig_fNHI[mt] == 1:
warnings.warn(
"Assuming the value for {:s}_{:s} is a lower limit".format(
fdict[key]['quasar'], fdict[key]['galaxy']))
#ax.quiver(orig_NHI[mt], fdict[key]['fit_NHI'][0], 1, 0,
# units='x', width=0.03, headwidth=2., headlength=5.)
elif orig_fNHI[mt] == 2:
pass
#ax.quiver(orig_NHI[mt], fdict[key]['fit_NHI'][0], 1, 0,
# units='x', width=0.03, headwidth=2., headlength=5.)
elif orig_fNHI[mt] == 3:
raise ValueError("Very Unlikely")
else:
raise ValueError("Nope")
# New
#xdb.set_trace()
yerr = [[fdict[key]['fit_NHI'][0] - fdict[key]['fit_NHI'][1]],
[fdict[key]['fit_NHI'][2] - fdict[key]['fit_NHI'][0]]]
ax.errorbar([orig_NHI[mt]], [fdict[key]['fit_NHI'][0]],
yerr=yerr,
capthick=2,
fmt='o')
# 1-1 line
ax.plot(NHI_mnx, NHI_mnx, ':', color='gray')
# End
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
pp.close()
plt.close()