def build_sys_from_dict(self, sys_name, llist=None, **kwargs): """ Build CGMAbsSys from the internal dict Parameters ---------- sys_name : str Name of the system llist : LineList, optional kwargs : passed to CGMAbsSys.from_dict Returns ------- CGMAbsSys """ tdict = self._dict[sys_name] cgmsys = CGMAbsSys.from_dict(tdict, chk_vel=False, chk_sep=False, chk_data=False, use_coord=True, use_angrho=True, linelist=llist, **kwargs) # Return return cgmsys
def cgm_from_galaxy_igmsystems(galaxy, igmsystems, R_max=300 * u.kpc, dv_max=400 * u.km / u.s, cosmo=None, **kwargs): """ Generate a list of CGMAbsSys objects given an input galaxy and a list of IGMSystems Parameters ---------- galaxy : Galaxy igmsystems : list list of IGMSystems R_max : Quantity Maximum projected separation from sightline to galaxy dv_max Maximum velocity offset between system and galaxy Returns ------- cgm_list : list list of CGM objects generated """ from pyigm.cgm.cgm import CGMAbsSys # Cosmology if cosmo is None: cosmo = cosmology.Planck15 # R rho, angles = calc_rho(galaxy, igmsystems, cosmo) # dv igm_z = np.array([igmsystem.zabs for igmsystem in igmsystems]) dv = ltu.dv_from_z(igm_z, galaxy.z) # Rules match = np.where((rho < R_max) & (np.abs(dv) < dv_max))[0] if len(match) == 0: print("No CGM objects match your rules") return [] else: # Loop to generate cgm_list = [] for imatch in match: cgm = CGMAbsSys(galaxy, igmsystems[imatch], cosmo=cosmo, **kwargs) cgm_list.append(cgm) # Return return cgm_list
def from_tarball(cls, tfile, debug=False, **kwargs): """ Load the COS-Halos survey from a tarball of JSON files Parameters ---------- tfile : str Returns ------- """ import tarfile import json from linetools.lists.linelist import LineList llist = LineList('ISM') slf = cls(**kwargs) # Load tar = tarfile.open(tfile) for kk, member in enumerate(tar.getmembers()): if '.' not in member.name: print('Skipping a likely folder: {:s}'.format(member.name)) continue # Debug if debug and (kk == 5): break # Extract f = tar.extractfile(member) tdict = json.load(f) # Generate cgmsys = CGMAbsSys.from_dict(tdict, chk_vel=False, chk_sep=False, chk_data=False, use_coord=True, use_angrho=True, linelist=llist, **kwargs) slf.cgm_abs.append(cgmsys) tar.close() # Return return slf
def p11(): """ Ingest Prochaska et al. 2011 CGM survey """ # Low z OVI summary ovi_file = pyigm.__path__[0] + '/data/CGM/P11/lowovidat.fits' ovidat = Table.read(ovi_file) qso_radec = SkyCoord(ra=ovidat['QSO_RA'], dec=ovidat['QSO_DEC'], unit=(u.hourangle, u.deg)) qso_nms = np.array([row['QSO'].strip() for row in ovidat]) # CGM Survey p11 = CGMAbsSurvey(survey='P11', ref='Prochaska+11') # Dwarfs cgm_dwarf_file = pyigm.__path__[0] + '/data/CGM/P11/dwarf_galabs_strct.fits' cgm_dwarfs = Table.read(cgm_dwarf_file) # sub L* cgm_subls_file = pyigm.__path__[0] + '/data/CGM/P11/subls_galabs_strct.fits' cgm_subls = Table.read(cgm_subls_file) # L* cgm_lstar_file = pyigm.__path__[0] + '/data/CGM/P11/lstar_galabs_strct.fits' cgm_lstar = Table.read(cgm_lstar_file) # Loop on subsets for subset in [cgm_dwarfs, cgm_subls, cgm_lstar]: for row in subset: # RA, DEC # Galaxy gal = Galaxy((row['RA'], row['DEC']), z=row['Z']) gal.Lstar = row['DDEC'] gal.type = row['GAL_TYPE'] # IGMSys mtqso = np.where(qso_nms == row['FIELD'].strip())[0] if len(mtqso) != 1: pdb.set_trace() raise ValueError("No Field match") igmsys = IGMSystem(qso_radec[mtqso[0]], row['Z'], (-400., 400.) * u.km / u.s) # HI if row['MAG'][2] > 0.: # Lya lya = AbsLine(1215.67 * u.AA, z=float(row['MAG'][3])) lya.attrib['EW'] = row['MAG'][4] / 1e3 * u.AA if row['MAG'][5] >= 99.: lya.attrib['flag_EW'] = 3 else: lya.attrib['flag_EW'] = 1 lya.attrib['sig_EW'] = row['MAG'][5] / 1e3 * u.AA # Ref lya.attrib['Ref'] = int(row['MAG'][2]) # HI component if row['MAG'][9] <= 0.: flagN = 3 elif row['MAG'][9] > 9.: flagN = 2 else: flagN = 1 HIcomp = AbsComponent(qso_radec[mtqso[0]], (1, 1), float(row['MAG'][3]), (-400, 400) * u.km / u.s, Ntup=(flagN, row['MAG'][8], row['MAG'][9])) HIcomp._abslines.append(lya) igmsys._components.append(HIcomp) # NHI igmsys.NHI = HIcomp.logN igmsys.flag_NHI = HIcomp.flag_N igmsys.sig_NHI = HIcomp.sig_N # OVI if row['MAGERR'][2] > 0.: # OVI 1031 ovi1031 = None if row['MAGERR'][4] > 0.: ovi1031 = AbsLine(1031.9261 * u.AA, z=float(row['MAGERR'][3])) if row['MAGERR'][5] >= 99.: ovi1031.attrib['flag_EW'] = 3 else: ovi1031.attrib['flag_EW'] = 1 ovi1031.attrib['EW'] = row['MAGERR'][4] / 1e3 * u.AA ovi1031.attrib['sig_EW'] = row['MAGERR'][5] / 1e3 * u.AA # OVI component if row['MAGERR'][9] <= 0.: flagN = 3 elif row['MAGERR'][9] > 9.: flagN = 2 else: flagN = 1 OVIcomp = AbsComponent(qso_radec[mtqso[0]], (8, 6), float(row['MAGERR'][3]), (-400, 400) * u.km / u.s, Ntup=(flagN, row['MAGERR'][8], row['MAGERR'][9])) if ovi1031 is not None: OVIcomp._abslines.append(ovi1031) # Ref OVIcomp.Ref = int(row['MAG'][2]) igmsys._components.append(OVIcomp) # CGM cgmabs = CGMAbsSys(gal, igmsys, chk_lowz=False) p11.cgm_abs.append(cgmabs) # Write tarball out_file = pyigm.__path__[0] + '/data/CGM/P11/P11_sys.tar' p11.to_json_tarball(out_file)
def ingest_johnson15(): """ Ingest Johnson+15 """ # Dict for QSO coords qsos = {} qsos['1ES1028+511'] = ltu.radec_to_coord('J103118.52517+505335.8193') qsos['FBQS1010+3003'] = ltu.radec_to_coord((152.5029167, 30.056111)) qsos['HE0226-4110'] = ltu.radec_to_coord('J022815.252-405714.62') qsos['HS1102+3441'] = ltu.radec_to_coord('J110539.8189+342534.672') qsos['LBQS1435-0134'] = ltu.radec_to_coord((219.451183, -1.786328)) qsos['PG0832+251'] = ltu.radec_to_coord('J083535.8048+245940.146') qsos['PG1522+101'] = ltu.radec_to_coord((231.1023075, 9.9749372)) qsos['PKS0405-123'] = ltu.radec_to_coord('J040748.4376-121136.662') qsos['SBS1108+560'] = ltu.radec_to_coord((167.8841667, 55.790556)) qsos['SBS1122+594'] = ltu.radec_to_coord((171.4741250, 59.172667)) qsos['Ton236'] = ltu.radec_to_coord((232.1691746, 28.424928)) # Virial matching j15_file = resource_filename('pyigm', 'data/CGM/z0/johnson2015_table1.fits') j15_tbl = Table.read(j15_file) # Clip COS-Halos keep = j15_tbl['Survey'] != 'COS-Halos' j15_tbl = j15_tbl[keep] # CGM Survey j15 = CGMAbsSurvey(survey='J15', ref='Johnson+15') # Linelist llist = LineList('ISM') for row in j15_tbl: # RA, DEC # Galaxy gal = Galaxy((row['RAJ2000'], row['DEJ2000']), z=float(row['zgal'])) gal.Class = row['Class'] gal.Mstar = row['logM_'] gal.field = row['Name'] gal.Env = row['Env'] gal.d_Rh = row['d_Rh'] # igmsys = IGMSystem(qsos[row['Name']], float(row['zgal']), (-400., 400.) * u.km / u.s) # HI if np.isnan(row['logNHI']): pass else: # HI component if row['l_logNHI'] == '<': flagN = 3 sigNHI = 99. elif np.isnan(row['e_logNHI']): flagN = 2 sigNHI = 99. else: flagN = 1 sigNHI = row['e_logNHI'] HIcomp = AbsComponent(qsos[row['Name']], (1, 1), float(row['zgal']), (-400, 400) * u.km / u.s, Ntup=(flagN, row['logNHI'], sigNHI)) igmsys._components.append(HIcomp) # NHI igmsys.NHI = HIcomp.logN igmsys.flag_NHI = HIcomp.flag_N igmsys.sig_NHI = HIcomp.sig_N # OVI if np.isnan(row['logNHOVI']): pass else: # OVI component if row['l_logNHOVI'] == '<': flagN = 3 sigNHOVI = 99. elif np.isnan(row['e_logNHOVI']): flagN = 2 sigNHOVI = 99. else: flagN = 1 sigNHOVI = row['e_logNHOVI'] OVIcomp = AbsComponent(qsos[row['Name']], (8, 6), float(row['zgal']), (-400, 400) * u.km / u.s, Ntup=(flagN, row['logNHOVI'], sigNHOVI)) igmsys._components.append(OVIcomp) # CGM cgmabs = CGMAbsSys(gal, igmsys, chk_lowz=False) j15.cgm_abs.append(cgmabs) # Write tarball out_file = resource_filename('pyigm', '/data/CGM/z0/J15_sys.tar') j15.to_json_tarball(out_file)
def ingest_burchett16(smthd='vir'): """ Ingest Burchett+16 """ # Virial matching if smthd == 'vir': b16_file = resource_filename( 'pyigm', 'data/CGM/z0/Burchett2016_CIV_HI_virselect.fits') else: b16_file = resource_filename( 'pyigm', 'data/CGM/z0/Burchett2016_CIV_HI_kpcselect.fits') b16_tbl = Table.read(b16_file) # CGM Survey b16 = CGMAbsSurvey(survey='B16', ref='Burchett+16') # Linelist llist = LineList('ISM') for row in b16_tbl: # RA, DEC # Galaxy gal = Galaxy((row['ra_gal'], row['dec_gal']), z=row['zgal']) gal.SFR = row['SFR'] gal.sig_SFR = row['SFR_err'] gal.Mstar = row['mstars'] gal.field = row['field'] gal.RRvir = row['rrvir'] gal.NSAidx = row['NSAidx'] # igmsys = IGMSystem((row['ra_qso'], row['dec_qso']), row['zgal'], (-400., 400.) * u.km / u.s) # HI if row['flag_h1'] > 0: # Lya lya = AbsLine(1215.67 * u.AA, z=row['zgal'], linelist=llist) lya.attrib['EW'] = row['EW_h1'] * u.AA lya.attrib['logN'] = row['col_h1'] lya.attrib['N'] = 10**row['col_h1'] * u.cm**-2 if row['flag_h1'] == 3: lya.attrib['flag_EW'] = 3 lya.attrib['flag_N'] = 3 lya.attrib['sig_N'] = (10**(row['col_h1'])) / 3. * u.cm**-2 elif row['flag_h1'] == 2: lya.attrib['flag_EW'] = 1 lya.attrib['flag_N'] = 2 else: lya.attrib['flag_EW'] = 1 lya.attrib['flag_N'] = 1 lya.attrib['sig_N'] = (10**(row['col_h1'] + row['colsig_h1']) - 10**row['col_h1']) * u.cm**-2 lya.attrib['sig_EW'] = row['EWsig_h1'] * u.AA # Ref lya.attrib['Ref'] = 'Burchett+16' # HI component if row['colsig_h1'] >= 99.: flagN = 2 elif row['colsig_h1'] <= 0.: flagN = 3 else: flagN = 1 HIcomp = AbsComponent( (row['ra_qso'], row['dec_qso']), (1, 1), row['zgal'], (-400, 400) * u.km / u.s, Ntup=(flagN, row['col_h1'], row['colsig_h1'])) HIcomp._abslines.append(lya) igmsys._components.append(HIcomp) # NHI igmsys.NHI = HIcomp.logN igmsys.flag_NHI = HIcomp.flag_N igmsys.sig_NHI = HIcomp.sig_N # CIV if row['flag_c4'] > 0: # CIV 1548 civ1548 = AbsLine(1548.195 * u.AA, z=row['zgal'], linelist=llist) civ1548.attrib['EW'] = row['EW_c4'] * u.AA civ1548.attrib['logN'] = row['col_c4'] civ1548.attrib['N'] = 10**row['col_c4'] * u.cm**-2 if row['flag_c4'] == 3: civ1548.attrib['flag_EW'] = 3 civ1548.attrib['flag_N'] = 3 civ1548.attrib['sig_N'] = (10**(row['col_c4'])) / 3. * u.cm**-2 elif row['flag_c4'] == 2: civ1548.attrib['flag_EW'] = 1 civ1548.attrib['flag_N'] = 2 else: civ1548.attrib['flag_EW'] = 1 civ1548.attrib['flag_N'] = 1 civ1548.attrib['sig_N'] = (10** (row['col_c4'] + row['colsig_c4']) - 10**row['col_c4']) * u.cm**-2 civ1548.attrib['sig_EW'] = row['EWsig_c4'] * u.AA # Ref civ1548.attrib['Ref'] = 'Burchett+16' # CIV component if row['colsig_c4'] >= 99.: flagN = 2 elif row['colsig_c4'] <= 0.: flagN = 3 else: flagN = 1 CIVcomp = AbsComponent( (row['ra_qso'], row['dec_qso']), (6, 4), row['zgal'], (-400, 400) * u.km / u.s, Ntup=(flagN, row['col_c4'], row['colsig_c4'])) CIVcomp._abslines.append(civ1548) igmsys._components.append(CIVcomp) # CGM cgmabs = CGMAbsSys(gal, igmsys, correct_lowz=False) b16.cgm_abs.append(cgmabs) # Write tarball if smthd == 'vir': out_file = resource_filename('pyigm', '/data/CGM/z0/B16_vir_sys.tar') else: out_file = resource_filename('pyigm', '/data/CGM/z0/B16_kpc_sys.tar') b16.to_json_tarball(out_file)
def cgm_from_galaxy_igmsystems(galaxy, igmsystems, rho_max=300 * u.kpc, dv_max=400 * u.km / u.s, cosmo=None, dummysys=False, dummyspec=None, verbose=True, **kwargs): """ Generate a list of CGMAbsSys objects given an input galaxy and a list of IGMSystems Parameters ---------- galaxy : Galaxy igmsystems : list list of IGMSystems rho_max : Quantity Maximum projected separation from sightline to galaxy dv_max Maximum velocity offset between system and galaxy dummysys: bool, optional If True, instantiate CGMAbsSys even if no match is found in igmsystems dummyspec : XSpectrum1D, optional Spectrum object to attach to dummy AbsLine/AbsComponent objects when adding IGMSystems if dummysys is True. Returns ------- cgm_list : list list of CGM objects generated """ from pyigm.cgm.cgm import CGMAbsSys # Cosmology if cosmo is None: cosmo = cosmology.Planck15 if dummysys is True: if dummyspec is None: dummyspec = igmsystems[0]._components[0]._abslines[0].analy['spec'] dummycoords = igmsystems[0].coord # R -- speed things up rho, angles = calc_cgm_rho(galaxy, igmsystems, cosmo, **kwargs) if len(igmsystems) == 1: # Kludge rho = u.Quantity([rho]) angles = u.Quantity([angles]) # dv igm_z = np.array([igmsystem.zabs for igmsystem in igmsystems]) dv = ltu.dv_from_z(igm_z, galaxy.z) # Rules match = np.where((rho < rho_max) & (np.abs(dv) < dv_max))[0] ### If none, see if some system has a component that's actually within dv_max if (len(match) == 0) & (rho[0] < rho_max): zcomps = [] sysidxs = [] for i, csys in enumerate(igmsystems): thesezs = [comp.zcomp for comp in csys._components] sysidxs.extend([i] * len(thesezs)) zcomps.extend(thesezs) zcomps = np.array(zcomps) sysidxs = np.array(sysidxs) dv_comps = ltu.dv_from_z(zcomps, galaxy.z) match = np.unique(sysidxs[np.where(np.abs(dv_comps) < dv_max)[0]]) if len(match) == 0: if dummysys is False: print( "No IGMSystem paired to this galaxy. CGM object not created.") return [] else: if verbose: print("No IGMSystem match found. Attaching dummy IGMSystem.") dummysystem = IGMSystem(dummycoords, galaxy.z, vlim=None) dummycomp = AbsComponent(dummycoords, (1, 1), galaxy.z, [-100., 100.] * u.km / u.s) dummycomp.flag_N = 3 dummyline = AbsLine( 'HI 1215', **kwargs) # Need an actual transition for comp check dummyline.analy['spec'] = dummyspec dummyline.attrib['coord'] = dummycoords dummycomp.add_absline(dummyline, chk_vel=False, chk_sep=False) dummysystem.add_component(dummycomp, chk_vel=False, chk_sep=False) cgm = CGMAbsSys(galaxy, dummysystem, cosmo=cosmo, **kwargs) cgm_list = [cgm] else: # Loop to generate cgm_list = [] for imatch in match: # Instantiate new IGMSystem # Otherwise, updates to the IGMSystem cross-pollinate other CGMs sysmatch = igmsystems[imatch] newisys = sysmatch.copy() # Handle z limits zlim = ltu.z_from_dv((-dv_max.value, dv_max.value) * u.km / u.s, galaxy.z) newlims = zLimits(galaxy.z, zlim.tolist()) newisys.limits = newlims # Allow for components extending beyond dv_max newisys.update_vlim() newisys.update_component_vel() # Finish cgm = CGMAbsSys(galaxy, newisys, cosmo=cosmo, rho=rho[imatch], ang_sep=angles[imatch], **kwargs) cgm_list.append(cgm) # Return return cgm_list
def load_tarball(self, tfile, build_data=True, build_sys=False, llist=None, verbose=True, **kwargs): """ Parameters ---------- tfile build_data build_sys llist kwargs Returns ------- """ import tarfile # Load tar = tarfile.open(tfile) for kk, member in enumerate(tar.getmembers()): if '.json' not in member.name: print('Skipping a likely folder: {:s}'.format(member.name)) continue # Extract f = tar.extractfile(member) try: tdict = json.load(f) except: if verbose: print('Unable to load {}'.format(member)) continue # Build dict self._dict[tdict['Name']] = tdict # Generate if build_sys: cgmsys = CGMAbsSys.from_dict(tdict, chk_vel=False, chk_sep=False, chk_data=False, use_coord=True, use_angrho=True, linelist=llist, **kwargs) self.cgm_abs.append(cgmsys) tar.close() # Galaxy coords ras = [self._dict[key]['RA'] for key in self._dict.keys()] decs = [self._dict[key]['DEC'] for key in self._dict.keys()] self.coords = SkyCoord(ra=ras, dec=decs, unit='deg') # Sightline coords ras = [self._dict[key]['igm_sys']['RA'] for key in self._dict.keys()] decs = [self._dict[key]['igm_sys']['DEC'] for key in self._dict.keys()] self.scoords = SkyCoord(ra=ras, dec=decs, unit='deg') # Data table if build_data: self.build_data_from_dict() # Return return
def load_coolgas(self): """ Load data on cool gas (CII, CIV, SiII, SiIII) Richter+17 """ llist = LineList('ISM') # Ricther+17 print('Loading Richter+17 for CII, CIV, SiII, SiIII') r17_a1_file = resource_filename('pyigm', '/data/CGM/Galaxy/richter17_A1.fits') r17_a1 = Table.read(r17_a1_file) r17_a2_file = resource_filename('pyigm', '/data/CGM/Galaxy/richter17_A2.fits') r17_a2 = Table.read(r17_a2_file) # Coords coords = SkyCoord(ra=r17_a1['_RAJ2000'], dec=r17_a1['_DEJ2000'], unit='deg') gc = coords.transform_to('galactic') ra = np.zeros((len(r17_a2))) dec = np.zeros((len(r17_a2))) # Loop on Sightlines for kk, row in enumerate(r17_a1): if self.debug and (kk == 5): break a2_idx = np.where(r17_a2['Name'] == row['Name'])[0] if len(a2_idx) == 0: continue ra[a2_idx] = row['_RAJ2000'] dec[a2_idx] = row['_DEJ2000'] # Generate the components icoord = gc[kk] alines = [] for jj, idx in enumerate(a2_idx): # Transition trans = '{:s} {:d}'.format(r17_a2['Ion'][idx].strip(), int(r17_a2['lambda0'][idx])) try: aline = AbsLine(trans, linelist=llist) except ValueError: pdb.set_trace() aline.attrib['coord'] = icoord # Skip EW=0 lines if r17_a2['e_W'][idx] == 0: continue # Velocity z = 0. aline.setz(z) vlim = np.array([r17_a2['vmin'][idx], r17_a2['vmax'][idx] ]) * u.km / u.s aline.limits.set(vlim) # These are v_LSR # EW aline.attrib['flag_EW'] = 1 aline.attrib['EW'] = r17_a2['W'][idx] / 1e3 * u.AA aline.attrib['sig_EW'] = r17_a2['e_W'][idx] / 1e3 * u.AA # Column if np.isnan( r17_a2['logN'] [idx]): # Odd that some lines had an error but no value aline.attrib['flag_N'] = 0 elif r17_a2['l_logN'][idx] == '>': aline.attrib['flag_N'] = 2 aline.attrib['sig_logN'] = 99.99 else: aline.attrib['flag_N'] = 1 aline.attrib['sig_logN'] = r17_a2['e_logN'][idx] aline.attrib['logN'] = r17_a2['logN'][idx] # Fill linear _, _ = linear_clm(aline.attrib) alines.append(aline) # Generate components from abslines comps = ltiu.build_components_from_abslines(alines, chk_sep=False, chk_vel=False) # Limits vmin = np.min([icomp.limits.vmin.value for icomp in comps]) vmax = np.max([icomp.limits.vmax.value for icomp in comps]) # Instantiate s_kwargs = dict(name=row['Name'] + '_z0') c_kwargs = dict(chk_sep=False, chk_z=False) abssys = IGMSystem.from_components(comps, vlim=[vmin, vmax] * u.km / u.s, s_kwargs=s_kwargs, c_kwargs=c_kwargs) # CGM Abs rho, ang_sep = calc_Galactic_rho(abssys.coord) cgmabs = CGMAbsSys(self.galaxy, abssys, rho=rho, ang_sep=ang_sep, cosmo=self.cosmo) # Add to cgm_abs self.abs.cgm_abs.append(cgmabs) # Finish r17_a2['RA'] = ra r17_a2['DEC'] = dec self.richter17 = r17_a2 # Reference if len(self.refs) > 0: self.refs += ',' self.refs += 'Richter+17'
def load_hotgas(self): """ Load data on hot gas (e.g. OVII, OVIII) Fang+15 """ # Init llist = LineList('EUV') ovii = AbsLine('OVII 21', linelist=llist) scoord = self.abs.scoord # Sightline coordiantes # Fang+15 Table 1 [OVII] fang15_file = resource_filename('pyigm', '/data/CGM/Galaxy/fang15_table1.dat') self.fang15 = Table.read(fang15_file, format='cds') print('Loading Fang+15 for OVII') # Reference if len(self.refs) > 0: self.refs += ',' self.refs += 'Fang+15' # Generate the systems # # (should check to see if low-ion ones exist already) for row in self.fang15: # Coordinates gc = SkyCoord(l=row['GLON'] * u.degree, b=row['GLAT'] * u.degree, frame='galactic') # Limits # OVII line aline = ovii.copy() aline.attrib['coord'] = gc z = row['Vel'] / c_kms try: aline.setz(z) except IOError: z = 0. vlim = np.array([-300, 300]) * u.km / u.s aline.attrib['flag_EW'] = 3 aline.attrib['EW'] = row['EW1'] / 1e3 * u.AA aline.attrib['sig_EW'] = 99. * u.AA # aline.attrib[ 'flag_N'] = 0 # Might be able to set an upper limit else: aline.attrib['b'] = row['b'] * u.km / u.s aline.attrib['flag_EW'] = 1 aline.attrib['EW'] = row['EW1'] / 1e3 * u.AA aline.attrib['sig_EW'] = row['e_EW1'] / 1e3 * u.AA vlim = np.array( [-1, 1]) * (2 * row['b'] + 2 * row['E_b']) * u.km / u.s # N_OVII aline.attrib['flag_N'] = 1 aline.attrib['logN'] = row['logNO'] aline.attrib['sig_logN'] = np.array( [row['e_logNO'], row['E_logNO']]) # Fill linear _, _ = linear_clm(aline.attrib) # OVII aline.limits.set(vlim) # Generate component and add comp = AbsComponent.from_abslines([aline]) if aline.attrib['flag_N'] == 0: # Hack to merge later comp.attrib['sig_logN'] = np.array([0., 0.]) else: pass # Check for existing system minsep = np.min(comp.coord.separation(scoord).to('arcsec')) if minsep < 30 * u.arcsec: # Add component to existing system idx = np.argmin(comp.coord.separation(scoord).to('arcsec')) if self.verbose: print("Adding OVII system to {}".format( self.abs.cgm_abs[idx].igm_sys)) self.abs.cgm_abs[idx].igm_sys.add_component(comp, chk_sep=False, debug=True) else: # Instantiate abssys = IGMSystem(gc, z, vlim, name=row['Name'] + '_z0', zem=row['z']) abssys.add_component(comp, chk_sep=False) # CGM Abs rho, ang_sep = calc_Galactic_rho(abssys.coord) cgmabs = CGMAbsSys(self.galaxy, abssys, rho=rho, ang_sep=ang_sep, cosmo=self.cosmo) # Add to cgm_abs self.abs.cgm_abs.append(cgmabs) scoord = self.abs.scoord # Sightline coordiantes # Savage+03 Table 2 [OVI] -- Thick disk/halo only?? print('Loading Savage+03 for OVI') savage03_file = resource_filename( 'pyigm', '/data/CGM/Galaxy/savage03_table2.fits') self.savage03 = Table.read(savage03_file) # Reference if len(self.refs) > 0: self.refs += ',' self.refs += 'Savage+03' # Generate the systems # # (should check to see if low-ion ones exist already) for row in self.savage03: # Coordinates coord = SkyCoord(ra=row['_RA'] * u.deg, dec=row['_DE'] * u.deg, frame='icrs') gc = coord.transform_to('galactic') # Build the component vlim = np.array([row['V-'], row['V_']]) * u.km / u.s comp = AbsComponent(gc, (8, 6), 0., vlim) # Add attributes if row['b'] > 0.: comp.attrib['vcen'] = row['__v_obs'] * u.km / u.s comp.attrib['sig_vcen'] = row['e__v_obs'] * u.km / u.s comp.attrib['b'] = row['b'] * u.km / u.s comp.attrib['sig_b'] = row['e_b'] * u.km / u.s # Column comp.attrib['flag_N'] = 1 comp.attrib['logN'] = row['logN_OVI_'] comp.attrib['sig_logN'] = np.array( [np.sqrt(row['e_sc']**2 + row['e_sys']**2)] * 2) else: # Upper limit comp.attrib['flag_N'] = 3 comp.attrib['logN'] = row['logN_OVI_'] comp.attrib['sig_logN'] = np.array([99.] * 2) # Set linear quantities _, _ = linear_clm(comp.attrib) # Check for existing system minsep = np.min(comp.coord.separation(scoord).to('arcsec')) if minsep < 30 * u.arcsec: idx = np.argmin(comp.coord.separation(scoord).to('arcsec')) self.abs.cgm_abs[idx].igm_sys.add_component(comp, chk_sep=False, debug=True, update_vlim=True) else: # New if row['RV'] > 0: zem = row['RV'] / c_kms else: zem = row['z'] abssys = IGMSystem(gc, comp.zcomp, vlim, name=row['Name'] + '_z0', zem=zem) abssys.add_component(comp, chk_sep=False, debug=True) # CGM Abs rho, ang_sep = calc_Galactic_rho(abssys.coord) cgmabs = CGMAbsSys(self.galaxy, abssys, rho=rho, ang_sep=ang_sep, cosmo=self.cosmo) # Add to cgm_abs self.abs.cgm_abs.append(cgmabs)