def meiring06(): '''Meiring et al. 2006, MNRAS, 370, 43 Q1107+0003 Taken from Table 4 by JXP NHI from RTN06 (damping wings) RA/DEC from STIS header ''' # Setup lls = LLSSystem(name='SDSSJ1107+0003_z0.954', RA=166.90273 * u.deg, Dec=0.05795000 * u.deg, zem=1.726, zabs=0.9542, vlim=[-300., 300.] * u.km / u.s, NHI=20.26, sigNHI=np.array([0.14, 0.09])) # Meiring06, Table 4 ion_dict = {} ion_dict['Zn II'] = dict(clm=12.08, sig_clm=0., flg_clm=3, Z=30, ion=2) ion_dict['Ti II'] = dict(clm=13.01, sig_clm=0., flg_clm=3, Z=22, ion=2) ion_dict['Cr II'] = dict(clm=12.76, sig_clm=0., flg_clm=3, Z=24, ion=2) # Finish lls._ionclms = IonClms(idict=ion_dict) lls.Refs.append('Mei06') return lls
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 test_parse_ion(): # JXP .ion file if os.getenv('LLSTREE') is None: assert True # Read datfil = 'Data/UM184.z2929.dat' lls = LLSSystem(dat_file=datfil, tree=os.getenv('LLSTREE')) # lls.get_ions() assert len(lls.lines) == 24
def add_LLS(self,z,NHI=17.3,bval=20.*u.km/u.s): '''Generate a new LLS ''' # new_sys = LLSSystem(NHI=NHI) new_sys.zabs = z new_sys.fill_lls_lines(bval=bval) # Name self.count_lls += 1 new_sys.label = 'LLS_Sys_{:d}'.format(self.count_lls) # Add self.abssys_widg.add_fil(new_sys.label) self.abssys_widg.all_abssys.append(new_sys) self.abssys_widg.abslist_widget.item( len(self.abssys_widg.all_abssys)).setSelected(True)
def test_dat_init(): # JXP .dat files if os.getenv('LLSTREE') is None: assert True # Read datfil = 'Data/UM184.z2929.dat' lls = LLSSystem(dat_file=datfil, tree=os.getenv('LLSTREE')) # np.testing.assert_allclose(lls.zabs, 2.93012)
def nestor08(): '''Nestor, D. et al. 2008, MNRAS, 390, 1670-1682 Q2149+212 Taken from Table 1 by JXP NHI from RTN06 (damping wings) RA/DEC from STIS header ''' # Setup lls = LLSSystem(name='SDSSJ2151+2130_z1.002', RA=327.94096 * u.deg, Dec=21.503750 * u.deg, zem=1.534, zabs=1.0023, vlim=[-300., 300.] * u.km / u.s, NHI=19.30, sigNHI=np.array([0.10, 0.10])) # Meiring06, Table 4 ion_dict = {} ion_dict['Zn II'] = dict(clm=12.13, sig_clm=0., flg_clm=3, Z=30, ion=2) ion_dict['Cr II'] = dict(clm=12.59, sig_clm=0., flg_clm=3, Z=24, ion=2) # Finish lls._ionclms = IonClms(idict=ion_dict) lls.Refs.append('Nes08') return lls
def add_LLS(self, z, NHI=17.3, bval=20. * u.km / u.s, comment='None'): '''Generate a new LLS ''' # new_sys = LLSSystem(NHI=NHI) new_sys.zabs = z new_sys.bval = bval # This is not standard, but for convenience new_sys.comment = comment new_sys.fill_lls_lines(bval=bval) # Name self.count_lls += 1 new_sys.label = 'LLS_Sys_{:d}'.format(self.count_lls) # Add self.abssys_widg.add_fil(new_sys.label) self.abssys_widg.all_abssys.append(new_sys) self.abssys_widg.abslist_widget.item(len( self.abssys_widg.all_abssys)).setSelected(True)
def add_LLS(self, z, NHI=17.3, bval=20.0 * u.km / u.s, comment="None"): """Generate a new LLS """ # new_sys = LLSSystem(NHI=NHI) new_sys.zabs = z new_sys.bval = bval # This is not standard, but for convenience new_sys.comment = comment new_sys.fill_lls_lines(bval=bval) # Name self.count_lls += 1 new_sys.label = "LLS_Sys_{:d}".format(self.count_lls) # Add self.abssys_widg.add_fil(new_sys.label) self.abssys_widg.all_abssys.append(new_sys) self.abssys_widg.abslist_widget.item(len(self.abssys_widg.all_abssys)).setSelected(True)
def add_LLS(self, z, NHI=17.3, bval=20. * u.km / u.s): '''Generate a new LLS ''' # new_sys = LLSSystem(NHI=NHI) new_sys.zabs = z new_sys.fill_lls_lines(bval=bval) # Name self.count_lls += 1 new_sys.label = 'LLS_Sys_{:d}'.format(self.count_lls) # Add self.abssys_widg.add_fil(new_sys.label) self.abssys_widg.all_abssys.append(new_sys) self.abssys_widg.abslist_widget.item(len( self.abssys_widg.all_abssys)).setSelected(True)
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] == '$<': ion_dict[ion] = dict(sig_clm=0., flg_clm=3, Z=Zion[0], ion=Zion[1]) ion_dict[ion]['clm'] = float(is2[2:7]) + NHI - 12 + sol[kk] elif is2[0:2] == '..': pass else: ion_dict[ion] = dict(flg_clm=1, Z=Zion[0], ion=Zion[1]) ion_dict[ion]['clm'] = float(is2[1:6]) + NHI - 12 + sol[kk] ion_dict[ion]['sig_clm'] = float(is2[10:14]) #xdb.set_trace() # Finish lls._ionclms = IonClms(idict=ion_dict) lls.Refs.append('DZ09') all_lls.append(lls) # Return SLLS only fin_slls = [ills for ills in all_lls if ills.NHI < 20.3] return fin_slls
def meiring09(): '''Meiring et al. 2009, MNRAS, 393, 1513 SLLS with Magellan Abundances from Table 3 from astro-ph (LateX) by JXP [AODM] RA/DEC from Table 1 ''' all_lls = [] # Table 1 tab_fil = xa_path + "/data/LLS/meiring09.tb1.ascii" with open(tab_fil, 'r') as f: flines1 = f.readlines() # Grab RA/DEC qso_dict = {} for iline in flines1: if iline[0:3] in [' QS', '\hl', '$\\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 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 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 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 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 xq100_plls_ex(outfil='fig_xq100_plls_ex.pdf'): # Load spectrum spec_fil = os.getenv('DROPBOX_DIR') + '/XQ-100/data/J0030-5159_uvb.fits' spec = load_spectrum(spec_fil) # Generate model model_file = os.getenv( 'DROPBOX_DIR') + '/XQ-100/LLS/convg_J0030-5159_llsfit.json' with open(model_file) as data_file: lls_dict = json.load(data_file) # Continuum basec = Quantity(lls_dict['conti']) telfer_spec = XSpectrum1D.from_tuple((spec.dispersion.value, basec.value)) # Start the plot if outfil is not None: pp = PdfPages(outfil) plt.figure(figsize=(8, 4)) plt.clf() gs = gridspec.GridSpec(1, 1) fsz = 17. # Read and plot full spectrum ax_full = plt.subplot(gs[0]) # Limits wvmnx = [3600., 5000.] gdpix = np.where(spec.dispersion < wvmnx[1] * u.AA)[0] perc = xsb.perc(spec.flux[gdpix]) ax_full.set_xlim(wvmnx) #ax_full.set_ylim(-0.05*perc[1], 1.1*perc[1]) ax_full.set_ylim(-1e-18, 4e-17) # Plot ax_full.plot(spec.dispersion, spec.flux, color='black', lw=1.0) ax_full.plot(wvmnx, [0., 0.], '--', color='green') # Label ax_full.set_xlabel('Wavelength') ax_full.set_ylabel('Relative Flux') ax_full.text(0.05, 0.9, 'XQ100 J0030-5159', transform=ax_full.transAxes, color='black', size='x-large', ha='left', va='center', bbox={'facecolor': 'white'}) all_ills = [] all_lls = [] all_zlls = [] for key in lls_dict['LLS'].keys(): new_sys = LLSSystem(NHI=lls_dict['LLS'][key]['NHI']) new_sys.zabs = lls_dict['LLS'][key]['z'] new_sys.fill_lls_lines(bval=lls_dict['LLS'][key]['bval'] * u.km / u.s) # all_ills.append(new_sys) all_lls.append(new_sys) all_zlls.append(new_sys.zabs) # Model norm_flux = lls_model(spec.dispersion, all_ills, smooth=lls_dict['smooth']) continuum = telfer_spec.flux * lls_dict['conti_model']['Norm'] * ( spec.dispersion.value / lls_dict['conti_model']['piv_wv'])**lls_dict['conti_model']['tilt'] # Model ax_full.plot(spec.dispersion, continuum * norm_flux) # Font size xputils.set_fontsize(ax_full, fsz) # Finish page plt.tight_layout(pad=0.2, h_pad=0.3, w_pad=0.0) pp.savefig() plt.close() print('Wrote: {:s}'.format(outfil)) # Finish pp.close()
def test_simple_init(): # Init lls = LLSSystem(NHI=17.9) # np.testing.assert_allclose(lls.NHI, 17.9)
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