def kacprzak12():
'''Kacprzak, G. et al. 2012, MNRAS, 427, 3029-3043
TON 153
Taken from Table 1 by JXP
NHI from Churchill+2007
RA/DEC from Simbad
'''
# Setup
radec = xor.stod1('J131956.2209+272808.271')
lls = LLSSystem(name='TON153_z1.002',
RA=radec[0],
Dec=radec[1],
zem=0.6610,
zabs=1.0023,
vlim=[-250., 200.] * u.km / u.s,
NHI=18.30,
sigNHI=np.array([0.30, 0.30]))
# Table 1 (total)
ion_dict = {}
ion_dict['Mg II'] = dict(clm=13.11, sig_clm=0.07, flg_clm=1, Z=12, ion=2)
ion_dict['Mg I'] = dict(clm=11.54, sig_clm=0.06, flg_clm=1, Z=12, ion=1)
ion_dict['Si I'] = dict(clm=11.8, sig_clm=0.00, flg_clm=3, Z=14, ion=1)
ion_dict['Si II'] = dict(clm=13.16, sig_clm=0.11, flg_clm=1, Z=14, ion=2)
ion_dict['Si IV'] = dict(clm=12.4, sig_clm=0.0, flg_clm=3, Z=14, ion=4)
ion_dict['C II'] = dict(clm=13.39, sig_clm=0.0, flg_clm=2, Z=6, ion=2)
ion_dict['C III'] = dict(clm=14.20, sig_clm=0.05, flg_clm=1, Z=6, ion=3)
ion_dict['C III'] = dict(clm=14.41, sig_clm=0.05, flg_clm=1, Z=6, ion=4)
ion_dict['O VI'] = dict(clm=14.49, sig_clm=0.05, flg_clm=1, Z=8, ion=6)
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Kcz12')
return lls
def zonak2004():
'''Zoank, S. et al. 2004, ApJ, 2004, 606, 196
PG1634+706
HST+Keck spectra
MgII, SiIV, SiIII from Table 2. Summing Subsystems A (Model 2) and B
Errors estimated by JXP (not reported)
SiIII in A may be a model
SiIV in B may be a model
Total NHI from LL. Taken from Fig 3 caption.
Error estimated by JXP
Not all EWs in Table 1 included
Adopting their M/H
'''
# Setup
radec = xor.stod1('J163428.9897+703132.422') # SIMBAD
lls = LLSSystem(name='PG1634+706_z1.041',
RA=radec[0],
Dec=radec[1],
zem=1.337,
zabs=1.0414,
vlim=[-200., 30.] * u.km / u.s,
NHI=17.23,
MH=-1.4,
sigNHI=np.array([0.15, 0.15]))
# SubSystems
lls.mk_subsys(2)
# Abundances
adict = dict(MgII={
'clm': log_sum([11.45, 11.90, 12.02, 11.68]),
'sig_clm': 0.05,
'flg_clm': 1
},
SiIII={
'clm': log_sum([12.5, 12.5, 12.8, 12.7]),
'sig_clm': 0.25,
'flg_clm': 1
},
SiIV={
'clm': log_sum([10.9, 10.8, 11.2, 11.1]),
'sig_clm': 0.15,
'flg_clm': 1
})
lls.subsys['A']._ionclms = IonClms(idict=adict)
bdict = dict(SiIII={
'clm': log_sum([11.8, 12.8, 12.4]),
'sig_clm': 0.15,
'flg_clm': 1
},
SiIV={
'clm': log_sum([11.2, 12.2, 11.8]),
'sig_clm': 0.15,
'flg_clm': 1
})
lls.subsys['B']._ionclms = IonClms(idict=bdict)
# Total
lls._ionclms = lls.subsys['A']._ionclms.sum(lls.subsys['B']._ionclms)
lls.Refs.append('Zon04')
# Return
return lls
def get_qso(self,inp):
'''Grab a QSO from the SDSS database
Similar to sdss_objinf in XIDL
Parameters:
----------
inp: tuple or str
tuple: (PLATE,FIBER)
string (JXXXXXX.X+XXXXXX.X format)
Returns:
----------
row: QTable
Single line from SDSS DR7 table
'''
# Branch on inp
if isinstance(inp,tuple):
mt = np.where( (self._data['PLATE']==inp[0]) &
(self._data['FIBERID']==inp[1]))[0]
elif isinstance(inp,basestring):
# Get RA/DEC
radec = xor.stod1(inp)
# Match
mt = np.where( (np.abs(self._data['RAOBJ']-radec[0].value)<5e-3) &
(np.abs(self._data['DECOBJ']-radec[1].value)<5e-3))[0]
else:
raise ValueError('SDSS_QUASAR: Bad input type')
# Parse and return
if len(mt) == 0:
if isinstance(inp,tuple):
if self.verbose:
print('Plate={:d}, FIBERID={:d} not found in SDSS-{:s}'.format(
inp[0],inp[1],self._version))
elif isinstance(inp,basestring):
if self.verbose:
print('Quasar {:s} not found in SDSS-{:s}'.format(inp,self._version))
return
elif len(mt) == 1:
self.index = mt[0] # Useful for SdssQso class
return self._data[mt]
else:
raise ValueError('Not expecting this')
def get_qso(self, inp):
"""Grab a QSO from the SDSS database
Similar to sdss_objinf in XIDL
Parameters:
----------
inp: tuple or str
tuple: (PLATE,FIBER)
string (JXXXXXX.X+XXXXXX.X format)
Returns:
----------
row: QTable
Single line from SDSS DR7 table
"""
# Branch on inp
if isinstance(inp, tuple):
mt = np.where((self._data["PLATE"] == inp[0]) & (self._data["FIBERID"] == inp[1]))[0]
elif isinstance(inp, basestring):
# Get RA/DEC
radec = xor.stod1(inp)
# Match
mt = np.where(
(np.abs(self._data["RAOBJ"] - radec[0].value) < 5e-3)
& (np.abs(self._data["DECOBJ"] - radec[1].value) < 5e-3)
)[0]
else:
raise ValueError("SDSS_QUASAR: Bad input type")
# Parse and return
if len(mt) == 0:
if isinstance(inp, tuple):
if self.verbose:
print("Plate={:d}, FIBERID={:d} not found in SDSS-{:s}".format(inp[0], inp[1], self._version))
elif isinstance(inp, basestring):
if self.verbose:
print("Quasar {:s} not found in SDSS-{:s}".format(inp, self._version))
return
elif len(mt) == 1:
self.index = mt[0] # Useful for SdssQso class
return self._data[mt]
else:
raise ValueError("Not expecting this")
def peroux06a():
'''Peroux, C. et al. 2006a, MNRAS, 372, 369
SDSS J0134+0051
One of her sample
Metal columns taken by JXP from Table 2 (no online data)
Total NHI from damping wings
'''
# Setup
radec = xor.stod1('J013405.75+005109.4') # SDSS Name
lls = LLSSystem(name='SDSSJ0134+0051_z0.842',
RA=radec[0],
Dec=radec[1],
zem=1.522,
zabs=0.842,
vlim=[-150., 150.] * u.km / u.s,
NHI=19.93,
sigNHI=np.array([0.15, 0.15]))
# Table 2
ion_dict = {}
N = np.sum(np.array([5.56, 12.6, 13.7, 23.5, 61.4, 39.8, 6, 9.14]) * 1e10)
sig = np.sqrt(
np.sum((np.array([2.32, 3.1, 3.68, 4.13, 8.02, 6.65, 3.37, 2.82]) *
1e10)**2))
ion_dict['Mg I'] = dict(clm=np.log10(N),
sig_clm=sig / N / np.log(10),
flg_clm=1,
Z=12,
ion=1)
ion_dict['Mg II'] = dict(clm=np.log10(5e13),
sig_clm=0.,
flg_clm=2,
Z=12,
ion=2)
N = np.sum(
np.array([8.17, 4.28, 32.1, 125, 710, 301, 893, 600, 263, 65.7]) *
1e11)
sig = np.sqrt(
np.sum((np.array(
[2.63, 1.40, 2.37, 8.6, 53.2, 28.4, 73.5, 61.7, 14.0, 2.95]) *
1e11)**2))
ion_dict['Fe II'] = dict(clm=np.log10(N),
sig_clm=sig / N / np.log(10),
flg_clm=1,
Z=26,
ion=2)
sig = np.sqrt(np.sum((np.array([3.72, 1.84, 2.36, 3.83]) * 1e11)**2))
ion_dict['Zn II'] = dict(clm=np.log10(2 * sig),
sig_clm=0.,
flg_clm=3,
Z=30,
ion=2)
sig = np.sqrt(np.sum((np.array([19.4, 9.79]) * 1e11)**2))
ion_dict['Cr II'] = dict(clm=np.log10(2 * sig),
sig_clm=0.,
flg_clm=3,
Z=24,
ion=2)
# Not including MnII. Appears as a detection but also given as a limit..
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Prx06a')
return lls
def tripp2005():
'''Tripp, T. et al. 2005, ApJ, 2005, 619, 714
PG 1216+069 (LLS in Virgo)
HST/STIS, FUSE
Metal columns parsed from Tables 2 and 3
Total NHI from damping wings
M/H from O/H
'''
# Grab ASCII files from ApJ
tab_fils = [
xa_path + "/data/LLS/tripp2005.tb3.ascii",
xa_path + "/data/LLS/tripp2005.tb2.ascii"
]
urls = [
'http://iopscience.iop.org/0004-637X/619/2/714/fulltext/60797.tb3.txt',
'http://iopscience.iop.org/0004-637X/619/2/714/fulltext/60797.tb2.txt'
]
for jj, tab_fil in enumerate(tab_fils):
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
url = urls[jj]
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = xor.stod1('J121920.9320+063838.476') # SIMBAD
lls = LLSSystem(name='PG1216+069_z0.006',
RA=radec[0],
Dec=radec[1],
zem=0.3313,
zabs=0.00632,
vlim=[-100., 100.] * u.km / u.s,
NHI=19.32,
MH=-1.6,
sigNHI=np.array([0.03, 0.03]))
#lls.mk_subsys(2)
# Columns
# Start with Table 3 (VPFIT)
with open(tab_fils[0], 'r') as f:
flines3 = f.readlines()
ion_dict = {}
for iline in flines3:
if (len(iline.strip()) == 0):
continue
isplit = iline.split('\t')
# Ion
flg = 2
if (len(isplit[0].strip()) > 0): # & (isplit[0][0] not in ['1','2']):
ipos = isplit[0].find('1')
ionc = isplit[0][0:ipos - 1].strip()
try:
Zion = xai.name_ion(ionc)
except KeyError:
xdb.set_trace()
flg = 1
# Column
csplit = isplit[3].split(' ')
clm = float(csplit[0])
sig = float(csplit[2])
if flg == 1:
ion_dict[ionc] = dict(clm=clm,
sig_clm=sig,
flg_clm=1,
Z=Zion[0],
ion=Zion[1])
else: # Add it in
tmp_dict = dict(clm=clm,
sig_clm=sig,
flg_clm=1,
Z=Zion[0],
ion=Zion[1])
logN, siglogN = xiai.sum_logN(ion_dict[ionc], tmp_dict)
ion_dict[ionc]['clm'] = logN
ion_dict[ionc]['sig_clm'] = siglogN
ions = ion_dict.keys()
# Now Table 2 for the extras
with open(tab_fils[1], 'r') as f:
flines2 = f.readlines()
# Trim the first 10 lines
flines2 = flines2[10:]
# Loop
for iline in flines2:
isplit = iline.split('\t')
#
ionc = isplit[0].strip()
if (len(ionc) == 0) or (ionc in ions):
continue
#
Zion = xai.name_ion(ionc)
ion_dict[ionc] = dict(Z=Zion[0], ion=Zion[1], sig_clm=0.)
if isplit[4][0] == '<':
ion_dict[ionc]['clm'] = float(isplit[4][1:])
ion_dict[ionc]['flg_clm'] = 3
else:
raise ValueError('Should not get here')
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Tri05')
return lls
def battisti12():
'''Battisti, A. et al. 2012, ApJ, 744, 93
HST/COS
QSO info from Table 1
Metal columns parsed from Table 3
NHI from Lya
'''
all_lls = []
# Grab ASCII files from ApJ
tab_fils = [
xa_path + "/data/LLS/battisti12.tb1.ascii",
xa_path + "/data/LLS/battisti12.tb3.ascii"
]
urls = [
'http://iopscience.iop.org/0004-637X/744/2/93/suppdata/apj413924t1_ascii.txt',
'http://iopscience.iop.org/0004-637X/744/2/93/suppdata/apj413924t3_ascii.txt'
]
for jj, tab_fil in enumerate(tab_fils):
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
url = urls[jj]
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# QSO info
with open(tab_fils[0], 'r') as f:
flines1 = f.readlines()
# Grab RA/DEC
all_idict = []
for iline in flines1:
if iline[0:2] != 'SD':
continue
# Parse
isplit = iline.split('\t')
name = isplit[0].split(' ')[1]
radec = xor.stod1(name)
zem = float(isplit[1].strip())
zabs = float(isplit[2].strip())
NHI = float(isplit[3].strip()[0:4])
sigNHI = np.array([float(isplit[3].strip()[11:])] * 2)
# Save
lls = LLSSystem(name=name,
RA=radec[0],
Dec=radec[1],
zem=zem,
zabs=zabs,
NHI=NHI,
sigNHI=sigNHI)
#
all_lls.append(lls)
all_idict.append({})
# Abundances
with open(tab_fils[1], 'r') as f:
flines3 = f.readlines()
flines3 = flines3[5:]
ion = None
for iline in flines3:
if ion == 'Ni II':
break
isplit = iline.split('\t')
if isplit[0] == 'C II*': # Skipping CII*
continue
# ion
ipos = -1
while (isplit[0][ipos] not in ['I', 'V']):
ipos -= 1
ion = isplit[0][0:ipos + 1 + len(isplit[0])]
Zion = xai.name_ion(ion)
# Loop on systems
for kk, iis in enumerate(isplit[1:-1]):
if iis.strip()[0] == '.':
continue
all_idict[kk][ion] = dict(Z=Zion[0], ion=Zion[1], sig_clm=0.)
if iis[0] == '>':
all_idict[kk][ion]['flg_clm'] = 2
all_idict[kk][ion]['clm'] = float(iis[1:6])
elif iis[0] == '<':
all_idict[kk][ion]['flg_clm'] = 3
all_idict[kk][ion]['clm'] = float(iis[1:])
else:
all_idict[kk][ion]['flg_clm'] = 1
all_idict[kk][ion]['clm'] = float(iis[0:5])
all_idict[kk][ion]['sig_clm'] = float(iis[-4:])
# Return SLLS only
for kk, lls in enumerate(all_lls):
try:
lls._ionclms = IonClms(idict=all_idict[kk])
except ValueError:
xdb.set_trace()
lls.Refs.append('Bat12')
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def tumlinson11():
'''Tumlinson, J. et al. 2011, ApJ, 733, 111
J1009+0713
HST/COS
Metal columns parsed from Table 1
NHI from LL+Lyman series (uncertain)
'''
# Grab ASCII file from ApJ
tab_fil = xa_path + "/data/LLS/tumlinson11.tb1.ascii"
url = 'http://iopscience.iop.org/0004-637X/733/2/111/suppdata/apj388927t1_ascii.txt'
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = xor.stod1('J100902.06+071343.8') # From paper
lls = LLSSystem(name='J1009+0713_z0.356',
RA=radec[0],
Dec=radec[1],
zem=0.456,
zabs=0.3558,
vlim=[-200., 250.] * u.km / u.s,
NHI=18.4,
sigNHI=np.array([0.41, 0.41]))
#lls.mk_subsys(2)
# Columns
# Start with Table 3 (VPFIT)
with open(tab_fil, 'r') as f:
flines1 = f.readlines()
# Trim
flines1 = flines1[18:]
#
ion_dict = {}
line_dict = dict(OI='1302',
OVI='1038',
MgII='2803^b',
SiII='1190',
CaII='3934',
FeII='2586')
ion = None
for iline in flines1:
isplit = iline.split('\t')
if ion == 'FeIII': # Last line
break
# Ion
is2 = isplit[0].split(' ')
ion = is2[0] + is2[1]
try:
gdl = line_dict[ion]
except:
pass
#print('Taking {:s}'.format(isplit[0]))
else:
if is2[2] != gdl:
continue
Zion = xai.name_ion(ion)
ion_dict[ion] = dict(clm=0.,
sig_clm=0.,
flg_clm=0,
Z=Zion[0],
ion=Zion[1])
# Combine components [could replace with SubSystems some day]
for iis in isplit[1:-1]:
# Upper limit
if (iis.strip()[0] == '<') & (ion_dict[ion]['flg_clm'] == 0):
ion_dict[ion]['flg_clm'] = 3
ion_dict[ion]['clm'] = float(iis[1:])
elif (iis.strip()[0] == '>'): # Saturated
ion_dict[ion]['flg_clm'] = 2
ion_dict[ion]['clm'] = log_sum(
[ion_dict[ion]['clm'],
float(iis[1:5])])
elif iis.strip()[0] in ['.', '<']:
pass
else:
if ion_dict[ion]['flg_clm'] == 2: # Add to saturated
ion_dict[ion]['clm'] = log_sum(
[ion_dict[ion]['clm'],
float(iis[0:4])])
else:
ion_dict[ion]['flg_clm'] = 1
obj = dict(clm=float(iis[0:4]), sig_clm=float(iis[-4:]))
# Add
N, sig = xiai.sum_logN(ion_dict[ion], obj)
ion_dict[ion]['clm'] = N
ion_dict[ion]['sig_clm'] = sig
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Tum11')
return lls
def meiring09():
'''Meiring et al. 2009, MNRAS, 393, 1513
SLLS with Magellan
Abundances from Table 3 from astro-ph (LateX) by JXP [AODM]
RA/DEC from Table 1
'''
all_lls = []
# Table 1
tab_fil = xa_path + "/data/LLS/meiring09.tb1.ascii"
with open(tab_fil, 'r') as f:
flines1 = f.readlines()
# Grab RA/DEC
qso_dict = {}
for iline in flines1:
if iline[0:3] in [' QS', '\hl', '$\\c', ' J2', ' ']:
continue
# Parse
isplit = iline.split('&')
#xdb.set_trace()
if '$' in isplit[3].strip():
isplit[3] = '-' + (isplit[3].strip())[3:]
radec = xor.stod1((isplit[2], isplit[3]))
# zem
zem = float(isplit[5].strip())
# Save
qso_dict[isplit[0].strip()] = dict(RA=radec[0], Dec=radec[1], zem=zem)
# Abundances (AODM)
# Table 3
tab_fil = xa_path + "/data/LLS/meiring09.tb3.ascii"
with open(tab_fil, 'r') as f:
flines3 = f.readlines()
#
ion_dict = {}
for iline in flines3:
if iline[0:2] in ['\h', ' ']:
continue
# Parse
isplit = iline.split('&')
# Ions
if iline[0:2] == 'QS':
ioncs = []
Zions = []
for iis in isplit[3:-1]: # Skipping HI
# Parse
#is2 = iis.split('\\')
#ip2 = is2[2].find('}')
ionc = iis.strip()
# Zion
Zion = xai.name_ion(ionc)
# Append
ioncs.append(ionc)
Zions.append(Zion)
continue
if iline[0] == 'Q':
# QSO
qso = isplit[0].strip()
if qso[-1] in ['A', 'B', 'C']:
qso = qso[0:-1]
# zabs and name
zabs = float(isplit[1].strip())
qso_dict[qso]['name'] = qso + 'z_{:.3f}'.format(zabs)
qso_dict[qso]['zabs'] = zabs
# NHI
is2 = isplit[2].strip()
if is2[0] == '$':
qso_dict[qso]['NHI'] = 99.99 # THROW OUT Q1436-0051B
qso_dict[qso]['sigNHI'] = np.array([0., 0.])
else:
qso_dict[qso]['NHI'] = float(is2[0:5])
qso_dict[qso]['sigNHI'] = np.array([float(is2[10:])] * 2)
#if qso_dict[qso]['NHI'] >= 20.3:
# print('Uh oh. DLA')
# Generate LLS
lls = LLSSystem(**qso_dict[qso])
continue
else:
# ADOM Columns
ion_dict = {}
for kk, iis in enumerate(isplit[3:-1]):
is2 = iis.strip()
if is2[0:3] == '$>$':
ion_dict[ioncs[kk]] = dict(sig_clm=0.,
flg_clm=2,
Z=Zions[kk][0],
ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[3:])
elif is2[0:3] == '$<$':
ion_dict[ioncs[kk]] = dict(sig_clm=0.,
flg_clm=3,
Z=Zions[kk][0],
ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[3:])
elif len(is2) == 0:
pass
else:
ion_dict[ioncs[kk]] = dict(flg_clm=1,
Z=Zions[kk][0],
ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[0:5])
ion_dict[ioncs[kk]]['sig_clm'] = float(is2[10:])
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Mei09')
all_lls.append(lls)
# Return SLLS only
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def test_tocoord():
from astropy.coordinates import SkyCoord
radec = x_r.stod1('J103138.87+255902.3')
coord = x_r.to_coord(radec)
#
assert isinstance(coord, SkyCoord)
def test_stod():
radec = x_r.stod1('J103138.87+255902.3')
np.testing.assert_allclose(radec[0].value, 157.91195833333336)
assert radec[0].unit == u.deg
def main(inp, survey='2r', radec=None, deci=None, fpath=None, show_circ=True,
EPOCH=0., DSS=None, BW=False, imsize=5.*astrou.arcmin, show_spec=False,
OUT_TYPE='PDF'):
'''
Parameters:
---------
inp: Input
string or List of strings or List of several items
'ra_dec_list.txt' -- ASCII file with columns of Name,RA,DEC and RA,DEC are string or float (deg)
['NAME_OF_TARG', '10:31:38.87', '+25:59:02.3']
['NAME_OF_TARG', 124.24*u.deg, -23.244*u.deg]
['NAME_OF_TARG', SkyCoord]
radec: integer (0) [DEPRECATED!]
Flag indicating type of input
0 = ASCII file with columns of Name,RA,DEC and RA,DEC are string or float (deg)
1 = List of string ['Name', 'RA', 'DEC']
2 = ['Name', ra_deg, dec_deg]
BW: bool (False)
B&W image?
show_circ: bool (True)
Show a yellow circle on the target
show_spec: bool (False)
Try to grab and show an SDSS spectrum
imsize: Quantity, optional
Image size
OUT_TYPE: str, optional
File type -- 'PDF', 'PNG'
'''
reload(x_r)
reload(xgs)
import matplotlib.pyplot as plt
import matplotlib.cm as cm
# Init
if fpath is None:
fpath = './'
try:
imsize=imsize.to('arcmin').value
except AttributeError:
raise AttributeError('finder: Input imsize needs to be an Angle')
cradius = imsize / 50.
# Read in the Target list
if isinstance(inp,basestring):
ra_tab = get_coord(targ_file, radec=radec)
else:
ira_tab = {}
ira_tab['Name'] = inp[0]
if isinstance(inp[1],basestring):
ra, dec = x_r.stod1((inp[1],inp[2]))
ira_tab['RA'] = ra
ira_tab['DEC'] = dec
elif isinstance(inp[1],float):
ira_tab['RA'] = inp[1] * astrou.deg
ira_tab['DEC'] = inp[2]* astrou.deg
elif isinstance(inp[1],SkyCoord):
ira_tab['RA'] = inp[1].ra.deg
ira_tab['DEC'] = inp[1].dec.deg
else: # Should check it is a Quantity
ira_tab['RA'] = inp[1]
ira_tab['DEC'] = inp[2]
# Strings
ras,decs = x_r.dtos1((ira_tab['RA'],ira_tab['DEC']))
ira_tab['RAS'] = ras
ira_tab['DECS'] = decs
# Make a list
ra_tab = [ira_tab]
# Grab ra, dec in decimal degrees
if deci is not None:
return
#xdb.set_trace()
#x_r.stod(ra_tab) #ra_tab['RA'][q], ra_tab['DEC'][q], TABL)
# Precess (as necessary)
if EPOCH > 1000.:
from astropy import units as u
from astropy.coordinates import FK5
from astropy.time import Time
# Precess to 2000.
tEPOCH = Time(EPOCH, format='jyear', scale='utc')
# Load into astropy
fk5c = FK5(ra=ra_tab['RA'], dec=ra_tab['DEC'], equinox=tEPOCH, unit=(u.degree,u.degree))
# Precess
newEPOCH = Time(2000., format='jyear', scale='utc')
newfk5 = fk5c.precess_to(newEPOCH)
# Save
ra_tab['RA'] = newfk5.ra.degree
ra_tab['DEC'] = newfk5.dec.degree
# Strings too?
ra_tab['RAS'] = str(newfk5.ra.to_string(unit=u.hour,sep=':'))
ra_tab['DECS'] = str(newfk5.dec.to_string(unit=u.hour,sep=':'))
##
# Main Loop
for obj in ra_tab:
# Outfil
nm = "".join(obj['Name'].split())
if OUT_TYPE=='PNG':
outfil = fpath+ nm + '.png'
else:
outfil = fpath+ nm + '.pdf'
print(outfil)
# Grab the Image
reload(xgs)
img, oBW = xgs.getimg(obj['RA'], obj['DEC'], imsize, BW=BW,DSS=DSS)
# Generate the plot
plt.clf()
fig = plt.figure(dpi=1200)
fig.set_size_inches(8.0,10.5)
# Font
plt.rcParams['font.family']= 'times new roman'
ticks_font = matplotlib.font_manager.FontProperties(family='times new roman',
style='normal', size=16, weight='normal', stretch='normal')
ax = plt.gca()
for label in ax.get_yticklabels() :
label.set_fontproperties(ticks_font)
for label in ax.get_xticklabels() :
label.set_fontproperties(ticks_font)
# Image
if oBW == 1:
cmm = cm.Greys_r
else:
cmm = None
plt.imshow(img,cmap=cmm,aspect='equal',extent=(-imsize/2., imsize/2, -imsize/2.,imsize/2))
# Axes
plt.xlim(-imsize/2., imsize/2.)
plt.ylim(-imsize/2., imsize/2.)
# Label
plt.xlabel('Relative ArcMin', fontsize=20)
xpos = 0.12*imsize
ypos = 0.02*imsize
plt.text(-imsize/2.-xpos, 0., 'EAST', rotation=90.,fontsize=20)
plt.text(0.,imsize/2.+ypos, 'NORTH', fontsize=20, horizontalalignment='center')
# Title
plt.text(0.5,1.24, str(nm), fontsize=32,
horizontalalignment='center',transform=ax.transAxes)
plt.text(0.5,1.16, 'RA (J2000) = '+str(obj['RAS']), fontsize=28,
horizontalalignment='center',transform=ax.transAxes)
plt.text(0.5,1.10, 'DEC (J2000) = '+str(obj['DECS']), fontsize=28,
horizontalalignment='center',transform=ax.transAxes)
#import pdb; pdb.set_trace()
# Circle
if show_circ:
circle=plt.Circle((0,0),cradius,color='y', fill=False)
plt.gca().add_artist(circle)
# Spectrum??
if show_spec:
spec_img = xgs.get_spec_img(obj['RA'], obj['DEC'])
plt.imshow(spec_img,extent=(-imsize/2.1, imsize*(-0.1), -imsize/2.1, imsize*(-0.2)))
# Write
if show_spec:
plt.savefig(outfil, dpi=300)
else:
plt.savefig(outfil)
print 'finder: Wrote '+outfil
plt.close()
#xdb.set_trace()
print 'finder: All done.'
return oBW
def main(inp,
survey='2r',
radec=None,
deci=None,
fpath=None,
show_circ=True,
EPOCH=0.,
DSS=None,
BW=False,
imsize=5. * astrou.arcmin,
show_spec=False,
OUT_TYPE='PDF',
show_another=None):
'''
Parameters:
---------
inp: Input
string or List of strings or List of several items
'ra_dec_list.txt' -- ASCII file with columns of Name,RA,DEC and RA,DEC are string or float (deg)
['NAME_OF_TARG', '10:31:38.87', '+25:59:02.3']
['NAME_OF_TARG', 124.24*u.deg, -23.244*u.deg]
['NAME_OF_TARG', SkyCoord]
radec: integer (0) [DEPRECATED!]
Flag indicating type of input
0 = ASCII file with columns of Name,RA,DEC and RA,DEC are string or float (deg)
1 = List of string ['Name', 'RA', 'DEC']
2 = ['Name', ra_deg, dec_deg]
BW: bool (False)
B&W image?
show_circ: bool (True)
Show a yellow circle on the target
show_another : tuple, optional
RA,DEC for another target to circle (e.g. offset star)
show_spec: bool (False)
Try to grab and show an SDSS spectrum
imsize: Quantity, optional
Image size
OUT_TYPE: str, optional
File type -- 'PDF', 'PNG'
'''
reload(x_r)
reload(xgs)
import matplotlib.pyplot as plt
import matplotlib.cm as cm
# Init
if fpath is None:
fpath = './'
try:
imsize = imsize.to('arcmin').value
except AttributeError:
raise AttributeError('finder: Input imsize needs to be an Angle')
cradius = imsize / 50.
# Read in the Target list
if isinstance(inp, basestring):
raise NotImplementedError("No longer implemented")
#ra_tab = get_coord(targ_file, radec=radec)
else:
ira_tab = {}
ira_tab['Name'] = inp[0]
if isinstance(inp[1], basestring):
ra, dec = x_r.stod1((inp[1], inp[2]))
ira_tab['RA'] = ra
ira_tab['DEC'] = dec
elif isinstance(inp[1], float):
ira_tab['RA'] = inp[1] * astrou.deg
ira_tab['DEC'] = inp[2] * astrou.deg
elif isinstance(inp[1], SkyCoord):
ira_tab['RA'] = inp[1].ra.deg
ira_tab['DEC'] = inp[1].dec.deg
else: # Should check it is a Quantity
ira_tab['RA'] = inp[1]
ira_tab['DEC'] = inp[2]
# Strings
ras, decs = x_r.dtos1((ira_tab['RA'], ira_tab['DEC']))
ira_tab['RAS'] = ras
ira_tab['DECS'] = decs
# Make a list
ra_tab = [ira_tab]
# Grab ra, dec in decimal degrees
if deci is not None:
return
#xdb.set_trace()
#x_r.stod(ra_tab) #ra_tab['RA'][q], ra_tab['DEC'][q], TABL)
# Precess (as necessary)
if EPOCH > 1000.:
from astropy import units as u
from astropy.coordinates import FK5
from astropy.time import Time
# Precess to 2000.
tEPOCH = Time(EPOCH, format='jyear', scale='utc')
# Load into astropy
fk5c = FK5(ra=ra_tab['RA'],
dec=ra_tab['DEC'],
equinox=tEPOCH,
unit=(u.degree, u.degree))
# Precess
newEPOCH = Time(2000., format='jyear', scale='utc')
newfk5 = fk5c.precess_to(newEPOCH)
# Save
ra_tab['RA'] = newfk5.ra.degree
ra_tab['DEC'] = newfk5.dec.degree
# Strings too?
ra_tab['RAS'] = str(newfk5.ra.to_string(unit=u.hour, sep=':'))
ra_tab['DECS'] = str(newfk5.dec.to_string(unit=u.hour, sep=':'))
##
# Main Loop
for obj in ra_tab:
# Outfil
nm = "".join(obj['Name'].split())
if OUT_TYPE == 'PNG':
outfil = fpath + nm + '.png'
else:
outfil = fpath + nm + '.pdf'
print(outfil)
# Grab the Image
reload(xgs)
img, oBW = xgs.getimg(obj['RA'], obj['DEC'], imsize, BW=BW, DSS=DSS)
# Generate the plot
plt.clf()
fig = plt.figure(dpi=1200)
fig.set_size_inches(8.0, 10.5)
# Font
plt.rcParams['font.family'] = 'times new roman'
ticks_font = matplotlib.font_manager.FontProperties(
family='times new roman',
style='normal',
size=16,
weight='normal',
stretch='normal')
ax = plt.gca()
for label in ax.get_yticklabels():
label.set_fontproperties(ticks_font)
for label in ax.get_xticklabels():
label.set_fontproperties(ticks_font)
# Image
if oBW == 1:
cmm = cm.Greys_r
else:
cmm = None
plt.imshow(img,
cmap=cmm,
aspect='equal',
extent=(-imsize / 2., imsize / 2, -imsize / 2., imsize / 2))
# Axes
plt.xlim(-imsize / 2., imsize / 2.)
plt.ylim(-imsize / 2., imsize / 2.)
# Label
plt.xlabel('Relative ArcMin', fontsize=20)
xpos = 0.12 * imsize
ypos = 0.02 * imsize
plt.text(-imsize / 2. - xpos, 0., 'EAST', rotation=90., fontsize=20)
plt.text(0.,
imsize / 2. + ypos,
'NORTH',
fontsize=20,
horizontalalignment='center')
#import pdb; pdb.set_trace()
# Circle
if show_circ:
circle = plt.Circle((0, 0), cradius, color='y', fill=False)
plt.gca().add_artist(circle)
# Second Circle
if show_another is not None:
# Coordinates
cobj = x_r.to_coord((obj['RA'], obj['DEC']))
canother = x_r.to_coord(show_another)
# Offsets
off, PA = x_r.offsets(cobj, canother)
xanother = -1 * off[0].to('arcmin').value
yanother = off[1].to('arcmin').value
square = matplotlib.patches.Rectangle(
(xanother - cradius, yanother - cradius),
cradius * 2,
cradius * 2,
color='cyan',
fill=False)
plt.gca().add_artist(square)
plt.text(0.5,
1.24,
str(nm),
fontsize=32,
horizontalalignment='center',
transform=ax.transAxes)
plt.text(0.5,
1.18,
'RA (J2000) = ' + str(obj['RAS']) + ' DEC (J2000) = ' +
str(obj['DECS']),
fontsize=22,
horizontalalignment='center',
transform=ax.transAxes)
plt.text(0.5,
1.12,
'RA(offset) = {:s} DEC(offset) = {:s}'.format(
canother.ra.to_string(unit=astrou.hour,
pad=True,
sep=':',
precision=2),
canother.dec.to_string(pad=True,
alwayssign=True,
sep=':',
precision=1)),
fontsize=22,
horizontalalignment='center',
transform=ax.transAxes,
color='blue')
plt.text(
0.5,
1.06,
'RA(offset to obj) = {:g} DEC(offset to obj) = {:g}'.format(
-1 * off[0].to('arcsec'), -1 * off[1].to('arcsec')),
fontsize=18,
horizontalalignment='center',
transform=ax.transAxes)
else:
# Title
plt.text(0.5,
1.24,
str(nm),
fontsize=32,
horizontalalignment='center',
transform=ax.transAxes)
plt.text(0.5,
1.16,
'RA (J2000) = ' + str(obj['RAS']),
fontsize=28,
horizontalalignment='center',
transform=ax.transAxes)
plt.text(0.5,
1.10,
'DEC (J2000) = ' + str(obj['DECS']),
fontsize=28,
horizontalalignment='center',
transform=ax.transAxes)
# Spectrum??
if show_spec:
spec_img = xgs.get_spec_img(obj['RA'], obj['DEC'])
plt.imshow(spec_img,
extent=(-imsize / 2.1, imsize * (-0.1), -imsize / 2.1,
imsize * (-0.2)))
# Write
if show_spec:
plt.savefig(outfil, dpi=300)
else:
plt.savefig(outfil)
print 'finder: Wrote ' + outfil
plt.close()
#xdb.set_trace()
print 'finder: All done.'
return oBW
def mmt_targets(field, path=None):
"""Read files related to MMT targets
Parameters:
-----------
field: tuple
(Name, ra, dec)
Returns:
----------
Target and observing info
"""
if path is None:
path = "/Galx_Spectra/MMT/"
# Targets
targ_path = field[0] + path
# Target file
targ_file = glob.glob(targ_path + "*.targ")
if len(targ_file) != 1:
raise ValueError("Wrong number of MMT target files")
else:
targ_file = targ_file[0]
# Read PI, program info [NOT IMPLEMENTED]
# f = open(msk_file, 'r')
# lines = f.readlines()
# f.close()
# Read target table
tab = ascii.read(targ_file, comment="#")
# Restrict to targets
itarg = np.where(tab["type"] == "TARGET")
targs = tab[itarg]
# Polish
nrow = len(targs)
targs.rename_column("ra", "RAS")
targs.rename_column("dec", "DECS")
targs.add_column(Column([0.0] * nrow, name="TARG_RA"))
targs.add_column(Column([0.0] * nrow, name="TARG_DEC"))
# Get RA/DEC in degrees
for k, row in enumerate(targs):
rad, decd = xra.stod1((row["RAS"], row["DECS"]))
targs[k]["TARG_RA"] = rad.value
targs[k]["TARG_DEC"] = decd.value
targs.rename_column("objid", "TARG_ID")
targs.rename_column("mag", "TARG_MAG")
targs.add_column(Column([0.0] * nrow, name="EPOCH"))
targs.add_column(Column(["SDSS"] * nrow, name="TARG_IMG"))
targs.add_column(Column(["HECTOSPEC"] * nrow, name="INSTR"))
targ_mask = {}
cnames = ["MASK_NAME", "MASK_ID"]
smsk = "--"
msk_val = [smsk] * len(cnames)
for kk, cname in enumerate(cnames):
targ_mask[cname] = [msk_val[kk]] * nrow
# Now the 'mask' files
mask_files = glob.glob(targ_path + "*.cat")
all_obs = []
all_masks = []
for mask_file in mask_files:
print("Reading MMT mask file: {:s}".format(mask_file))
i0 = mask_file.rfind("/")
mask_nm = mask_file[i0 + 1 : mask_file.find(".cat")]
# Grab info from spectrum file
# xdb.set_trace()
spec_fil = glob.glob(mask_file[: i0 + 1] + "spHect-" + mask_nm + "*.fits.gz")
if len(spec_fil) != 1:
print("spec_fil -- Not found!".format(spec_fil))
ras, decs = xra.dtos1((field[1], field[2]))
pa = 0.0
else:
header = fits.open(spec_fil[0])[0].header
if header["APERTURE"] != mask_nm:
raise ValueError("Mask doesnt match!")
pa = header["POSANGLE"]
ras = header["CAT-RA"]
decs = header["CAT-DEC"]
# Continuing
mask_dict = dict(
INSTR="HECTOSPEC", MASK_NAME=mask_nm, MASK_RA=ras, MASK_DEC=decs, MASK_EPOCH=2000.0, MASK_PA=pa
) # SHOULD GRAB PA, RA, DEC FROM SPECTRA FITS HEADER
all_masks.append(mask_dict)
# Read obs
f = open(mask_file, "r")
lines = f.readlines()
f.close()
iall_obs = []
for line in lines:
if "OBS" in line:
prs = line.strip().split(" ")
gdprs = [iprs for iprs in prs if len(iprs) > 0]
obs_dict = {}
obs_dict["DATE"] = gdprs[2]
obs_dict["TEXP"] = float(gdprs[3])
obs_dict["DISPERSER"] = gdprs[4]
obs_dict["CONDITIONS"] = gdprs[5]
#
iall_obs.append(obs_dict)
obs_tab = xxul.dict_list_to_table(iall_obs)
obs_tab["TEXP"].unit = u.s
# Read observed targets
obs_targ = ascii.read(mask_file, comment="#")
gdt = np.where(obs_targ["flag"] == 1)[0]
for gdi in gdt:
mtt = np.where(targs["TARG_ID"] == int(obs_targ["objid"][gdi]))[0]
if len(mtt) != 1:
raise ValueError("Multiple matches?!")
targ_mask["MASK_NAME"][mtt[0]] = mask_nm
all_obs.append(obs_tab)
# Finish
mask = np.array([False] * len(targs))
bad = np.where(np.array(targ_mask["names"]) == "--")[0]
if len(bad) > 0:
mask[bad] = True
#
clm = MaskedColumn(targ_mask["names"], name="MASK_NAME", mask=mask)
targs.add_column(clm)
return all_masks, all_obs, targs
def main(inp,
survey='2r',
radec=None,
deci=None,
fpath=None,
EPOCH=0.,
DSS=None,
BW=False,
imsize=5.,
show_spec=False):
'''
Parameters:
---------
inp: Input
string or List of strings or List of several items
'ra_dec_list.txt' -- ASCII file with columns of Name,RA,DEC and RA,DEC are string or float (deg)
['NAME_OF_TARG', '10:31:38.87', '+25:59:02.3']
['NAME_OF_TARG', 124.24*u.deg, -23.244*u.deg]
radec: integer (0) [DEPRECATED!]
Flag indicating type of input
0 = ASCII file with columns of Name,RA,DEC and RA,DEC are string or float (deg)
1 = List of string ['Name', 'RA', 'DEC']
2 = ['Name', ra_deg, dec_deg]
BW: bool (False)
B&W image?
show_spec: bool (False)
Try to grab and show an SDSS spectrum
imsize: float
Image size in arcmin
'''
reload(x_r)
reload(xgs)
import matplotlib.pyplot as plt
import matplotlib.cm as cm
# Init
if fpath is None:
fpath = './'
cradius = imsize / 50.
# Read in the Target list
if isinstance(inp, basestring):
ra_tab = get_coord(targ_file, radec=radec)
else:
ira_tab = {}
ira_tab['Name'] = inp[0]
if isinstance(inp[1], basestring):
ra, dec = x_r.stod1((inp[1], inp[2]))
ira_tab['RA'] = ra
ira_tab['DEC'] = dec
elif isinstance(inp[1], float):
ira_tab['RA'] = inp[1] * astrou.deg
ira_tab['DEC'] = inp[2] * astrou.deg
else: # Should check it is a Quantity
ira_tab['RA'] = inp[1]
ira_tab['DEC'] = inp[2]
# Strings
ras, decs = x_r.dtos1((ira_tab['RA'], ira_tab['DEC']))
ira_tab['RAS'] = ras
ira_tab['DECS'] = decs
# Make a list
ra_tab = [ira_tab]
# Grab ra, dec in decimal degrees
if deci is not None:
return
#xdb.set_trace()
#x_r.stod(ra_tab) #ra_tab['RA'][q], ra_tab['DEC'][q], TABL)
# Precess (as necessary)
if EPOCH > 1000.:
from astropy import units as u
from astropy.coordinates import FK5
from astropy.time import Time
# Precess to 2000.
tEPOCH = Time(EPOCH, format='jyear', scale='utc')
# Load into astropy
fk5c = FK5(ra=ra_tab['RA'],
dec=ra_tab['DEC'],
equinox=tEPOCH,
unit=(u.degree, u.degree))
# Precess
newEPOCH = Time(2000., format='jyear', scale='utc')
newfk5 = fk5c.precess_to(newEPOCH)
# Save
ra_tab['RA'] = newfk5.ra.degree
ra_tab['DEC'] = newfk5.dec.degree
# Strings too?
ra_tab['RAS'] = str(newfk5.ra.to_string(unit=u.hour, sep=':'))
ra_tab['DECS'] = str(newfk5.dec.to_string(unit=u.hour, sep=':'))
##
# Main Loop
for obj in ra_tab:
# Outfil
nm = "".join(obj['Name'].split())
outfil = fpath + nm + '.pdf'
print(outfil)
# Grab the Image
reload(xgs)
img, oBW = xgs.getimg(obj['RA'], obj['DEC'], imsize, BW=BW, DSS=DSS)
# Generate the plot
plt.clf()
fig = plt.figure(dpi=1200)
fig.set_size_inches(8.0, 10.5)
# Font
plt.rcParams['font.family'] = 'times new roman'
ticks_font = matplotlib.font_manager.FontProperties(
family='times new roman',
style='normal',
size=16,
weight='normal',
stretch='normal')
ax = plt.gca()
for label in ax.get_yticklabels():
label.set_fontproperties(ticks_font)
for label in ax.get_xticklabels():
label.set_fontproperties(ticks_font)
# Image
if oBW == 1:
cmm = cm.Greys_r
else:
cmm = None
plt.imshow(img,
cmap=cmm,
aspect='equal',
extent=(-imsize / 2., imsize / 2, -imsize / 2., imsize / 2))
# Axes
plt.xlim(-imsize / 2., imsize / 2.)
plt.ylim(-imsize / 2., imsize / 2.)
# Label
plt.xlabel('Relative ArcMin', fontsize=20)
xpos = 0.12 * imsize
ypos = 0.02 * imsize
plt.text(-imsize / 2. - xpos, 0., 'EAST', rotation=90., fontsize=20)
plt.text(0.,
imsize / 2. + ypos,
'NORTH',
fontsize=20,
horizontalalignment='center')
# Title
plt.text(0.5,
1.24,
str(nm),
fontsize=32,
horizontalalignment='center',
transform=ax.transAxes)
plt.text(0.5,
1.16,
'RA (J2000) = ' + str(obj['RAS']),
fontsize=28,
horizontalalignment='center',
transform=ax.transAxes)
plt.text(0.5,
1.10,
'DEC (J2000) = ' + str(obj['DECS']),
fontsize=28,
horizontalalignment='center',
transform=ax.transAxes)
#import pdb; pdb.set_trace()
# Circle
circle = plt.Circle((0, 0), cradius, color='y', fill=False)
plt.gca().add_artist(circle)
# Spectrum??
if show_spec:
spec_img = xgs.get_spec_img(obj['RA'], obj['DEC'])
plt.imshow(spec_img,
extent=(-imsize / 2.1, imsize * (-0.1), -imsize / 2.1,
imsize * (-0.2)))
# Write
if show_spec:
plt.savefig(outfil, dpi=300)
else:
plt.savefig(outfil)
print 'finder: Wrote ' + outfil
#xdb.set_trace()
print 'finder: All done.'
return oBW
def test_stod():
radec = x_r.stod1('J103138.87+255902.3')
np.testing.assert_allclose(radec[0].value, 157.91195833333336)
assert radec[0].unit == u.deg
def peroux06b():
'''Peroux, C. et al. 2006b, A&A, 450, 53
SDSS J1323-0021
Metal rich
Metal columns copied by JXP from Table 1
Total NHI from damping wings
'''
# Setup
radec = xor.stod1('J132323.78-002155.2') # SDSS Name
lls = LLSSystem(name='SDSSJ1323-0021_z0.716',
RA=radec[0],
Dec=radec[1],
zem=1.390,
zabs=0.716,
vlim=[-200., 200.] * u.km / u.s,
NHI=20.21,
sigNHI=np.array([0.20, 0.20]))
# Parse table file
tab_fil = xa_path + "/data/LLS/peroux06b.tb1.ascii"
with open(tab_fil, 'r') as f:
flines = f.readlines()
ion_dict = {}
for iline in flines:
isplit = iline.split('\t')
if len(isplit[0]) == 0:
# Grab ions and init
ions = isplit[3:10]
for ion in ions:
Zion = xai.name_ion(ion)
ion_dict[ion] = dict(clm=0.,
sig_clm=0.,
flg_clm=1,
Z=Zion[0],
ion=Zion[1])
continue
# Column or sigma?
if isplit[0][0] == 'N': # Column
for kk, iis in enumerate(isplit[3:10]):
ion = ions[kk]
if iis[0] == '>':
ion_dict[ion]['flg_clm'] = 2
ion_dict[ion]['clm'] += float(iis[1:])
elif iis[0] == '<':
pass
elif iis[0] == '.':
pass
else:
ion_dict[ion]['clm'] += float(iis)
else: # Sigma
for kk, iis in enumerate(isplit[3:10]):
ion = ions[kk]
if iis[0] == '.':
pass
else:
ion_dict[ion]['sig_clm'] += float(iis)**2
# Convert to log
for ion in ions:
N = ion_dict[ion]['clm']
sig = np.sqrt(ion_dict[ion]['sig_clm'])
#
ion_dict[ion]['clm'] = np.log10(N)
if ion_dict[ion]['flg_clm'] == 2:
ion_dict[ion]['sig_clm'] = 0.
else:
ion_dict[ion]['sig_clm'] = sig / N / np.log(10)
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Prx06b')
return lls
def test_tocoord():
from astropy.coordinates import SkyCoord
radec = x_r.stod1('J103138.87+255902.3')
coord = x_r.to_coord(radec)
#
assert isinstance(coord,SkyCoord)
def dessauges09():
'''Dessauges-Zavadsky et al. 2009, MNRAS, 396, L96
SLLS with UVES
Zn,Fe abundances from Table 1 from astro-ph (LateX) by JXP [AODM]
Taken from the Zn/H and Fe/H assuming *no* ionization corrections
RA/DEC from the 'other' name
'''
# Solar abundances
eZn = 4.63
eFe = 7.45
sol = [eFe, eZn]
#
all_lls = []
# Table 1
tab_fil = xa_path + "/data/LLS/dessauges09.tb1.ascii"
with open(tab_fil, 'r') as f:
flines1 = f.readlines()
# Trim the first few lines
flines1 = flines1[3:]
ion_dict = {}
for iline in flines1:
# Parse
isplit = iline.split('&')
# QSO
if iline[0:2] == 'QS':
# QSO, RA/DEC, zem
qso = isplit[0][4:].strip()
radec = xor.stod1(isplit[1].strip().replace('$', ''))
zem = float(isplit[3].strip())
# NHI, zabs
zabs = float(isplit[4].strip())
is2 = isplit[6].strip()
NHI = float(is2[1:6])
sigNHI = np.array([float(is2[10:14])] * 2)
# name
name = qso + 'z_{:.3f}'.format(zabs)
lls = LLSSystem(name=name,
RA=radec[0],
Dec=radec[1],
zem=zem,
zabs=zabs,
NHI=NHI,
sigNHI=sigNHI)
# ADOM Columns
ion_dict = {}
for kk, ion in enumerate(['Fe II', 'Zn II']):
Zion = xai.name_ion(ion)
is2 = isplit[7 + kk].strip()
if is2[0:2] == '$>':
ion_dict[ion] = dict(sig_clm=0.,
flg_clm=2,
Z=Zion[0],
ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[2:7]) + NHI - 12 + sol[kk]
elif is2[0:2] == '$<':
ion_dict[ion] = dict(sig_clm=0.,
flg_clm=3,
Z=Zion[0],
ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[2:7]) + NHI - 12 + sol[kk]
elif is2[0:2] == '..':
pass
else:
ion_dict[ion] = dict(flg_clm=1, Z=Zion[0], ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[1:6]) + NHI - 12 + sol[kk]
ion_dict[ion]['sig_clm'] = float(is2[10:14])
#xdb.set_trace()
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('DZ09')
all_lls.append(lls)
# Return SLLS only
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def jenkins2005():
'''Jenkins, E. et al. 2005, ApJ, 2005, 623, 767
PHL 1811
HST/STIS, FUSE
Metals parsed from Table 1
OI taken from text
Had to input error on columns by hand (JXP)
Total NHI from Lyman series. see Fig 3
M/H from O/H
'''
# Grab ASCII file from ApJ
tab_fil = xa_path + "/data/LLS/jenkins2005.tb1.ascii"
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
url = 'http://iopscience.iop.org/0004-637X/623/2/767/fulltext/61520.tb1.txt'
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = xor.stod1('J215501.5152-092224.688') # SIMBAD
lls = LLSSystem(name='PHL1811_z0.081',
RA=radec[0],
Dec=radec[1],
zem=0.192,
zabs=0.080923,
vlim=[-100., 100.] * u.km / u.s,
NHI=17.98,
MH=-0.19,
sigNHI=np.array([0.05, 0.05]))
# AbsLines
ism = LineList('ISM')
Nsig = {
'C IV': 0.4,
'N II': 0.4,
'Si II': 0.05,
'Si IV': 0.25,
'S II': 0.2,
'Fe II': 0.12,
'H I': 0.05,
'S III': 0.06
}
# Parse Table
with open(tab_fil, 'r') as f:
flines = f.readlines()
ion_dict = {}
for iline in flines:
iline = iline.strip()
if (len(iline) == 0):
continue
# Split on tabs
isplit = iline.split('\t')
# Offset?
ioff = 0
if isplit[0][0] in ['1', '2']:
ioff = -1
# Catch bad lines
if (isplit[1 + ioff][0:6]
in ['1442.0', '1443.7',
'1120.9']): # Skip goofy CII line and CII*
continue
if len(isplit[2 + ioff]) == 0:
continue
# Ion
if (len(isplit[0].strip()) > 0) & (isplit[0][0] not in ['1', '2']):
ionc = isplit[0].strip()
try:
Zion = xai.name_ion(ionc)
except KeyError:
xdb.set_trace()
# Generate the Line
try:
newline = AbsLine(float(isplit[2 + ioff]) * u.AA,
linelist=ism,
closest=True)
except ValueError:
xdb.set_trace()
newline.attrib['z'] = lls.zabs
# Spectrum
newline.analy['datafile'] = 'STIS' if 'S' in isplit[1] else 'FUSE'
# EW
try:
EWvals = isplit[4 + ioff].split(' ')
except IndexError:
xdb.set_trace()
newline.attrib['EW'] = float(EWvals[0]) * u.AA / 1e3
newline.attrib['EWsig'] = float(EWvals[2]) * u.AA / 1e3
newline.attrib['flgEW'] = 1
if len(isplit) < (5 + ioff + 1):
continue
# Colm?
#xdb.set_trace()
if (len(isplit[5 + ioff].strip()) > 0) & (isplit[5 + ioff].strip() !=
'\\ldots'):
if isplit[5 + ioff][0] == '\\':
ipos = isplit[5 + ioff].find(' ')
newline.attrib['N'] = float(isplit[5 + ioff][ipos + 1:])
newline.attrib['flagN'] = 2
elif isplit[5 + ioff][0] == '<':
ipos = 0
newline.attrib['N'] = float(isplit[5 + ioff][ipos + 1:])
newline.attrib['flagN'] = 3
elif isplit[5 + ioff][0] == '1':
try:
newline.attrib['N'] = float(isplit[5 + ioff][0:5])
except ValueError:
xdb.set_trace()
newline.attrib['flagN'] = 1
try:
newline.attrib['Nsig'] = Nsig[ionc]
except KeyError:
print('No error for {:s}'.format(ionc))
else:
raise ValueError('Bad character')
# ion_dict
ion_dict[ionc] = dict(clm=newline.attrib['N'],
sig_clm=newline.attrib['Nsig'],
flg_clm=newline.attrib['flagN'],
Z=Zion[0],
ion=Zion[1])
# Append
lls.lines.append(newline)
# Fix NI, OI
ion_dict['O I']['clm'] = 14.47
ion_dict['O I']['sig_clm'] = 0.05
ion_dict['N I']['flg_clm'] = 3
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Jen05')
# Return
return lls
def mmt_targets(field, path=None):
'''Read files related to MMT targets
Parameters:
-----------
field: tuple
(Name, ra, dec)
Returns:
----------
Target and observing info
'''
if path is None:
path = '/Galx_Spectra/MMT/'
# Targets
targ_path = field[0] + path
# Target file
targ_file = glob.glob(targ_path + '*.targ')
if len(targ_file) != 1:
raise ValueError('Wrong number of MMT target files')
else:
targ_file = targ_file[0]
# Read PI, program info [NOT IMPLEMENTED]
#f = open(msk_file, 'r')
#lines = f.readlines()
#f.close()
# Read target table
tab = ascii.read(targ_file, comment='#')
# Restrict to targets
itarg = np.where(tab['type'] == 'TARGET')
targs = tab[itarg]
# Polish
nrow = len(targs)
targs.rename_column('ra', 'RAS')
targs.rename_column('dec', 'DECS')
targs.add_column(Column([0.] * nrow, name='TARG_RA'))
targs.add_column(Column([0.] * nrow, name='TARG_DEC'))
# Get RA/DEC in degrees
for k, row in enumerate(targs):
rad, decd = xra.stod1((row['RAS'], row['DECS']))
targs[k]['TARG_RA'] = rad.value
targs[k]['TARG_DEC'] = decd.value
targs.rename_column('objid', 'TARG_ID')
targs.rename_column('mag', 'TARG_MAG')
targs.add_column(Column([0.] * nrow, name='EPOCH'))
targs.add_column(Column(['SDSS'] * nrow, name='TARG_IMG'))
targs.add_column(Column(['HECTOSPEC'] * nrow, name='INSTR'))
targ_mask = {}
cnames = ['MASK_NAME', 'MASK_ID']
smsk = '--'
msk_val = [smsk] * len(cnames)
for kk, cname in enumerate(cnames):
targ_mask[cname] = [msk_val[kk]] * nrow
# Now the 'mask' files
mask_files = glob.glob(targ_path + '*.cat')
all_obs = []
all_masks = []
for mask_file in mask_files:
print('Reading MMT mask file: {:s}'.format(mask_file))
i0 = mask_file.rfind('/')
mask_nm = mask_file[i0 + 1:mask_file.find('.cat')]
# Grab info from spectrum file
#xdb.set_trace()
spec_fil = glob.glob(mask_file[:i0 + 1] + 'spHect-' + mask_nm +
'*.fits.gz')
if len(spec_fil) != 1:
print('spec_fil -- Not found!'.format(spec_fil))
ras, decs = xra.dtos1((field[1], field[2]))
pa = 0.
else:
header = fits.open(spec_fil[0])[0].header
if header['APERTURE'] != mask_nm:
raise ValueError('Mask doesnt match!')
pa = header['POSANGLE']
ras = header['CAT-RA']
decs = header['CAT-DEC']
# Continuing
mask_dict = dict(
INSTR='HECTOSPEC',
MASK_NAME=mask_nm,
MASK_RA=ras,
MASK_DEC=decs,
MASK_EPOCH=2000.,
MASK_PA=pa) # SHOULD GRAB PA, RA, DEC FROM SPECTRA FITS HEADER
all_masks.append(mask_dict)
# Read obs
f = open(mask_file, 'r')
lines = f.readlines()
f.close()
iall_obs = []
for line in lines:
if 'OBS' in line:
prs = line.strip().split(' ')
gdprs = [iprs for iprs in prs if len(iprs) > 0]
obs_dict = {}
obs_dict['DATE'] = gdprs[2]
obs_dict['TEXP'] = float(gdprs[3])
obs_dict['DISPERSER'] = gdprs[4]
obs_dict['CONDITIONS'] = gdprs[5]
#
iall_obs.append(obs_dict)
obs_tab = xxul.dict_list_to_table(iall_obs)
obs_tab['TEXP'].unit = u.s
# Read observed targets
obs_targ = ascii.read(mask_file, comment='#')
gdt = np.where(obs_targ['flag'] == 1)[0]
for gdi in gdt:
mtt = np.where(targs['TARG_ID'] == int(obs_targ['objid'][gdi]))[0]
if len(mtt) != 1:
raise ValueError('Multiple matches?!')
targ_mask['MASK_NAME'][mtt[0]] = mask_nm
all_obs.append(obs_tab)
# Finish
mask = np.array([False] * len(targs))
bad = np.where(np.array(targ_mask['names']) == '--')[0]
if len(bad) > 0:
mask[bad] = True
#
clm = MaskedColumn(targ_mask['names'], name='MASK_NAME', mask=mask)
targs.add_column(clm)
return all_masks, all_obs, targs
def deimos_targets(field, gc=None, outfil=None, replot=True,
reset_layers=False):
'''
Call with gc to speed things up
'''
import matplotlib.cm as cm
import matplotlib.patches as patches
reload(xra)
# Init
# Mask dimensions
smsk_dim = (7., 16.6) # arcmin (approximate)
smsk_ang = np.arctan(smsk_dim[0]/smsk_dim[1])
smsk_diag = np.sqrt(smsk_dim[0]**2 + smsk_dim[1]**2)/2.
all_smsk_ang = [-1.*smsk_ang, smsk_ang, np.pi-smsk_ang, np.pi+smsk_ang]
# Coordinates
fcoord = SkyCoord(ra=field[1],dec=field[2])
if outfil is None:
outfil = xcasu.get_filename(field,'DEIMOS_TARG_FIG')
# Load field
lfield = xcasl.load_field(field)
targ_coord = SkyCoord(ra=lfield.targets['TARG_RA']*u.deg,
dec=lfield.targets['TARG_DEC']*u.deg)
all_pa = fcoord.position_angle(targ_coord)
all_sep = fcoord.separation(targ_coord).to('arcmin')
# Targets
deimos_targ = np.where(lfield.targets['INSTR'] == 'DEIMOS')[0]
#dra = all_sep[deimos_targ]*np.sin(all_pa[deimos_targ])
#ddec = all_sep[deimos_targ]*np.cos(all_pa[deimos_targ])
# Image
path = os.getenv('CASBAH_GALAXIES')
img_fil = path+'/'+field[0]+'/'+lfield.targets[deimos_targ]['TARG_IMG'][0]
gfil = glob.glob(img_fil+'*')
if len(gfil) != 1:
raise ValueError('Image not found! {:s}'.format(img_fil))
else:
img_fil = gfil[0]
#hdu = fits.open(img_fil)
#w = wcs.WCS(hdu[0].header,fix=True)
#img = hdu[0].data
'''
# Size
pix_qso = w.wcs_world2pix(np.array([[field[1].value,field[2].value]]), 1)
corners = [ [0.,0.], [0.,img.shape[0]], [img.shape[1],0.], [img.shape[1],img.shape[0]]]
rad_corners = w.wcs_pix2world(np.array(corners), 1) # deg but no units
mx_rad = [0.,0.]
for rad in rad_corners:
c_off, _ = xra.offsets(fcoord, tuple(rad))
for ii in range(2):
mx_rad[ii] = np.maximum(
mx_rad[ii],np.abs(c_off[ii].to('arcmin').value))
imsize = 2.*np.maximum(mx_rad[0],mx_rad[1])
'''
# Start the plot
#if outfil is not None:
# pp = PdfPages(outfil)
# Targets only
plt.figure(figsize=(8, 4.9))
plt.clf()
plt.suptitle('{:s}: DEIMOS Targets (from LBT imaging)'.format(field[0])
,fontsize=19.)
# Plot the Image
if gc is None:
gc = aplpy.FITSFigure(img_fil)
radius = 25./60/2. #0.01 # deg
if replot:
gc.recenter(field[1].value, field[2].value,radius=radius)
# This next one is a bit expensive
gc.show_grayscale(vmin=300., vmax=3000.,stretch='arcsinh',invert='True')
# Masks
msk_clrs = ['blue', 'red', 'green', 'orange']
deimos_obs = lfield.observing[np.where(
lfield.observing['INSTR']=='DEIMOS')[0]]
unimsk = np.unique(np.array(deimos_obs['MASK_NAME']))
for ii,msk in enumerate(unimsk):
mt = np.where(deimos_obs['MASK_NAME'] == msk)[0]
if not deimos_obs['DATE_OBS'].mask[mt[0]]:
# RA,DEC offset of center
mask_rad = xra.stod1((deimos_obs['MASK_RA'][mt[0]],
deimos_obs['MASK_DEC'][mt[0]]))
mask_pa = deimos_obs['MASK_PA'][mt[0]]*np.pi/180.
# RA/DEC offsets of corners
rect_x = [smsk_diag*np.sin(smsk_ang+mask_pa) for smsk_ang in all_smsk_ang]
rect_y = [smsk_diag*np.cos(smsk_ang+mask_pa) for smsk_ang in all_smsk_ang]
#xdb.set_trace()
prect_y = mask_rad[1].value + np.array(rect_y+[rect_y[0]])/60.
prect_x = mask_rad[0].value + np.array(rect_x+[rect_x[0]])/60./np.cos(prect_y*np.pi/180.)
'''
coord0 = SkyCoord(ra=prect_x[0]*u.deg,dec=prect_y[0]*u.deg)
coord2 = SkyCoord(ra=prect_x[2]*u.deg,dec=prect_y[2]*u.deg)
rcoord0 = SkyCoord(ra=rect_x[0]*u.arcmin,dec=rect_y[0]*u.arcmin)
rcoord2 = SkyCoord(ra=rect_x[2]*u.arcmin,dec=rect_y[2]*u.arcmin)
sep02 = coord0.separation(coord2).to('arcmin')
rsep02 = rcoord0.separation(rcoord2).to('arcmin')
print(sep02)
print(rsep02)
print(smsk_diag*2.)
xdb.set_trace()
'''
# Reshape
xy = np.zeros((2,5))
xy[0,:] = prect_x
xy[1,:] = prect_y
#xdb.set_trace()
gc.show_lines([xy],color=msk_clrs[ii])#,alpha=0.5)
# Markers
# Observed targets
sub_targ = np.where((lfield.targets['MASK_NAME']==msk)
& (lfield.targets['INSTR']=='DEIMOS'))[0]
obs_targ_tab, obs_dict, obs_idx = lfield.get_observed(radius*u.deg,
subtab=lfield.targets[sub_targ])
ra_obs_targ = lfield.targets[sub_targ[obs_idx]]['TARG_RA']
dec_obs_targ = lfield.targets[sub_targ[obs_idx]]['TARG_DEC']
gc.show_markers(ra_obs_targ, dec_obs_targ, edgecolor=msk_clrs[ii],
facecolor='none', marker='o', s=50)#, alpha=0.5)
# QSO
gc.show_markers(field[1].value, field[2].value, edgecolor='lightgreen', facecolor='none',
marker='s', s=10, alpha=0.5)
# Label
#gc.add_label(field[1].value, field[2].value, 'Q', color='green')
if outfil != None:
gc.save(outfil)
'''
